Protein transport-associated molecules

ABSTRACT

The invention provides human protein transport molecules (PTAM) and polynucleotides which identify and encode PTAM. The invention also provides expression vectors, host cells, antibodies, agonists, and antagonists. The invention also provides methods for diagnosing, treating, or preventing disorders associated with expression of PTAM.

This application is the National Stage of International Application No.PCT/US99/19616, filed on Aug. 26, 1999, which claims the benefit under35 U.S.C. § 119(e) of U.S. Provisional Application Ser. No. 60/098,206,filed Aug. 27, 1998, the contents all of which are hereby incorporatedherein by reference.

TECHNICAL FIELD

This invention relates to nucleic acid and amino acid sequences ofprotein transport-associated molecules and to the use of these sequencesin the diagnosis, treatment, and prevention of cell proliferative andsecretory disorders.

BACKGROUND OF THE INVENTION

The organization of a cell is designed for optimal structure andfunction. Each molecule produced by the cell must be targeted to theappropriate subcellular location. To be properly localized, eachmolecule must contain information which provides its cellular address.Trafficking machinery can use this information to appropriatelytransport the molecule to its destination. This is a dynamic process,and the location of a molecule can change over time. Defects in any stepinvolving a molecule's proper localization can result in a disorder,such as diabetes or Alzheimer's disease. (James, D. E., and Piper, R. C.(1994) J. Cell Biol. 126:1123-1126; and Nordstedt, C., et al. (1993) J.Biol. Chem. 268:608-612.)

The information that provides the address for targeting resides withinthe primary structure of the protein. Certain amino acid sequences actas “delivery codes” during the processing or recycling of a molecule andassure that the molecule is properly localized. Several motifs have beenidentified. The two principal motifs are the nuclear localization signaland signal peptide. Nuclear localization signals (NLS) consist of shortstretches of amino acids enriched in basic residues. NLS are found onproteins that are targeted to the nucleus, such as the glucocorticoidreceptor. The NLS is recognized by the NLS receptor, importin, whichthen interacts with the monomeric GTP-binding protein Ran. This NLSprotein/receptor/Ran complex navigates the nuclear pore with the help ofthe homodimeric protein nuclear transport factor 2 (NTF2). NTF2 binds tothe GDP-bound form of Ran and to multiple proteins of the nuclear porecomplex, such as p62.

Signal peptides are found on proteins that are targeted to theendoplasmic reticulum (ER). Signal peptides consist of stretches ofamino acids enriched in hydrophobic residues. Signal peptides areusually found at the extreme N-terminus of the protein and arerecognized by a cytosolic signal-recognition peptide (SRP). The SRPbinds to the signal peptide and to an SRP receptor, an integral membraneprotein in the ER. Once bound to the SRP receptor, the newly formedprotein containing the signal peptide is translocated across the ERmembrane. Proteins containing signal peptides may end up inserted intothe lipid bilayer, or they may end up in the lumen of an organelle orsecreted from the cell.

Proteins may also contain separate motifs that specify delivery orretention in a subcellular location. For example, the trans-Golginetwork integral membrane protein TGN38 cycles between the trans-Golginetwork (TGN) and the plasma membrane. TGN38 contains two separatemotifs. One motif, located within the cytoplasmic tail, is responsiblefor delivery to the Golgi. A second motif, located within thehydrophobic membrane-spanning region, is responsible for retention ofthe protein in the TGN. (Stephens, D. J., et al. (1997) J. Biol. Chem.272:14104-14109.) Modification of the motif may alter the address for aprotein and cause it to be relocalized. For example, plasma membranereceptors, such as the epidermal growth factor (EGF) receptor and theT-cell receptor (TCR), contain targeting motifs which, when ligand bindsto the receptor, become phosphorylated. Phosphorylation of the targetingmotif results in internalization and delivery of the receptor to thelysosome for degradation. (Dietrich, J. et al. (1994) EMBO J.13:2156-2166.)

The information provided by the amino acid motifs is used by thetrafficking machinery to sequester and package the protein intovesicles, and then deliver it to the appropriate location. Sortingnexin-1 (SNX1) is an example of a protein involved in the recognition ofmotifs involved in lysosomal targeting. Molecules targeted for thelysosome that require SNX1 include the carboxypeptidase Y sortingreceptor and the EGF receptor. In the absence of SNX1, these moleculesbecome mislocalized. (Kurten, R. C., Cadena, D. L., and Gill, G. N.(1996) Science 272:1008-1010; and Horazdovsky, B. F. et al. (1997) Mol.Biol. Cell 8:1529-1541.) The adaptor protein (AP) complex, whichtriggers assembly of clathrin on membranes to form vesicles, is alsoinvolved in sequestration of proteins for delivery to subcellularlocations. AP-1 vesicles, which form at the Golgi, includecation-independent and cation-dependent mannose-6-phosphate receptors(MPRs). These vesicles are delivered to the lysosome. AP-2 vesicles,which form at the plasma membrane, include TGN38 (Stephens, supra) andligand-bound TCR (Dietrich, supra.) TGN38-containing vesicles aredelivered to the TGN and TCR-containing vesicles are delivered to thelysosome.

Once molecules containing targeting motifs have been sequestered andpackaged into vesicles, the vesicles need to be delivered to theappropriate location. This delivery process involves another set ofproteins. The Rab family of GTPases are involved in this process via amechanism not clearly understood. Several Rab proteins have beendescribed, each associated with a particular organelle. For example,Rab3 is associated with the plasma membrane, Rab4 with the sortingendosome, and Rab11 with the recycling endosome. There are also Rabsspecific to cell types and functions. For example, Rab3A is specificallyinvolved in synaptic vesicle exocytosis in stimulated nerve cells, andRab4b is involved in glucose transporter-4 (GluT4) translocation ininsulin-stimulated adipocytes. (James and Piper, supra.)

The discovery of new protein transport associated molecules and thepolynucleotides encoding them satisfies a need in the art by providingnew compositions which are useful in the diagnosis, prevention, andtreatment of cell proliferative and secretory disorders.

SUMMARY OF THE INVENTION

The invention features substantially purified polypeptides, proteintransport-associated molecules, referred to collectively as “PTAM”. Inone aspect, the invention provides a substantially purified polypeptidecomprising an amino acid sequence selected from the group consisting ofSEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ IDNO:6, SEQ ID NO:7, SEQ ID NO:8 (SEQ ID NO: 1-8), and fragments thereof.

The invention further provides a substantially purified variant havingat least 90% amino acid identity to at least one of the amino acidsequences selected from the group consisting of SEQ ID NO:1-8, andfragments thereof. The invention also provides an isolated and purifiedpolynucleotide encoding the polypeptide comprising an amino acidsequence selected from the group consisting of SEQ ID NO:1-8, andfragments thereof. The invention also includes an isolated and purifiedpolynucleotide variant having at least 90% polynucleotide sequenceidentity to the polynucleotide encoding the polypeptide comprising anamino acid sequence selected from the group consisting of SEQ ID NO:1-8,and fragments thereof.

Additionally, the invention provides an isolated and purifiedpolynucleotide which hybridizes under stringent conditions to thepolynucleotide encoding the polypeptide comprising an amino acidsequence selected from the group consisting of SEQ ID NO:1-8, andfragments thereof. The invention also provides an isolated and purifiedpolynucleotide having a sequence which is complementary to thepolynucleotide encoding the polypeptide comprising the amino acidsequence selected from the group consisting of SEQ ID NO:1-8, andfragments thereof.

The invention also provides an isolated and purified polynucleotidecomprising a polynucleotide sequence selected from the group consistingof SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13,SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16 (SEQ ID NO:9-16), and fragmentsthereof. The invention further provides an isolated and purifiedpolynucleotide variant having at least 90% polynucleotide sequenceidentity to the polynucleotide sequence selected from the groupconsisting of SEQ ID NO:9-6, and fragments thereof. The invention alsoprovides an isolated and purified polynucleotide having a sequence whichis complementary to the polynucleotide comprising a polynucleotidesequence selected from the group consisting of SEQ ID NO:9-16, andfragments thereof.

The invention also provides a method for detecting a polynucleotide in asample containing nucleic acids, the method comprising the steps of (a)hybridizing the complement of the polynucleotide sequence to at leastone of the polynucleotides of the sample, thereby forming ahybridization complex; and (b) detecting the hybridization complex,wherein the presence of the hybridization complex correlates with thepresence of a polynucleotide in the sample. In one aspect, the methodfurther comprises amplifying the polynucleotide prior to hybridization.

The invention further provides an expression vector containing at leasta fragment of the polynucleotide encoding the polypeptide comprising anamino acid sequence selected from the group consisting of SEQ ID NO:1-8,and fragments thereof. In another aspect, the expression vector iscontained within a host cell.

The invention also provides a method for producing a polypeptide, themethod comprising the steps of: (a) culturing the host cell containingan expression vector containing at least a fragment of a polynucleotideunder conditions suitable for the expression of the polypeptide; and (b)recovering the polypeptide from the host cell culture.

The invention also provides a pharmaceutical composition comprising asubstantially purified polypeptide having the amino acid sequenceselected from the group consisting of SEQ ID NO:1-8, and fragmentsthereof, in conjunction with a suitable pharmaceutical carrier.

The invention further includes a purified antibody which binds to apolypeptide selected from the group consisting of SEQ ID NO:1-8, andfragments thereof. The invention also provides a purified agonist and apurified antagonist to the polypeptide.

The invention also provides a method for treating or preventing adisorder associated with decreased expression or activity of PTAM, themethod comprising administering to a subject in need of such treatmentan effective amount of a pharmaceutical composition comprising asubstantially purified polypeptide having the amino acid sequenceselected from the group consisting of SEQ ID NO:1-8, and fragmentsthereof, in conjunction with a suitable pharmaceutical carrier.

The invention also provides a method for treating or preventing adisorder associated with increased expression or activity of PTAM, themethod comprising administering to a subject in need of such treatmentan effective amount of an antagonist of a polypeptide having an aminoacid sequence selected from the group consisting of SEQ ID NO:1-8, andfragments thereof.

BRIEF DESCRIPTION OF THE TABLES

Table 1 shows nucleotide and polypeptide sequence identification numbers(SEQ ID NO), clone identification numbers (clone ID), cDNA libraries,and cDNA fragments used to assemble full-length sequences encoding PTAM.

Table 2 shows features of each polypeptide sequence including potentialmotifs, homologous sequences, and methods and algorithms used foridentification of PTAM.

Table 3 shows the tissue-specific expression patterns of each nucleicacid sequence as determined by northern analysis, diseases or disordersassociated with these tissues, and the vector into which each cDNA wascloned.

Table 4 describes the tissues used to construct the cDNA libraries fromwhich Incyte cDNA clones encoding PTAM were isolated.

Table 5 shows the programs, their descriptions, references, andthreshold parameters used to analyze PTAM.

DESCRIPTION OF THE INVENTION

Before the present proteins, nucleotide sequences, and methods aredescribed, it is understood that this invention is not limited to theparticular machines, materials and methods described, as these may vary.It is also to be understood that the terminology used herein is for thepurpose of describing particular embodiments only, and is not intendedto limit the scope of the present invention which will be limited onlyby the appended claims.

It must be noted that as used herein and in the appended claims, thesingular forms “a,” “an,” and “the” include plural reference unless thecontext clearly dictates otherwise. Thus, for example, a reference to “ahost cell” includes a plurality of such host cells, and a reference to“an antibody” is a reference to one or more antibodies and equivalentsthereof known to those skilled in the art, and so forth.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meanings as commonly understood by one of ordinary skillin the art to which this invention belongs. Although any machines,materials, and methods similar or equivalent to those described hereincan be used to practice or test the present invention, the preferredmachines, materials and methods are now described. All publicationsmentioned herein are cited for the purpose of describing and disclosingthe cell lines, protocols, reagents and vectors which are reported inthe publications and which might be used in connection with theinvention. Nothing herein is to be construed as an admission that theinvention is not entitled to antedate such disclosure by virtue of priorinvention.

Definitions

“PTAM” refers to the amino acid sequences of substantially purified PTAMobtained from any species, particularly a mammalian species, includingbovine, ovine, porcine, murine, equine, and preferably the humanspecies, from any source, whether natural, synthetic, semi synthetic, orrecombinant.

The term “agonist” refers to a molecule which, when bound to PTAM,increases or prolongs the duration of the effect of PTAM. Agonists mayinclude proteins, nucleic acids, carbohydrates, or any other moleculeswhich bind to and modulate the effect of PTAM.

An “allelic variant” is an alternative form of the gene encoding PTAM.Allelic variants may result from at least one mutation in the nucleicacid sequence and may result in altered mRNAs or in polypeptides whosestructure or function may or may not be altered. Any given natural orrecombinant gene may have none, one, or many allelic forms. Commonmutational changes which give rise to allelic variants are generallyascribed to natural deletions, additions, or substitutions ofnucleotides. Each of these types of changes may occur alone, or incombination with the others, one or more times in a given sequence.

“Altered” nucleic acid sequences encoding PTAM include those sequenceswith deletions, insertions, or substitutions of different nucleotides,resulting in a polynucleotide the same as PTAM or a polypeptide with atleast one functional characteristic of PTAM. Included within thisdefinition are polymorphisms which may or may not be readily detectableusing a particular oligonucleotide probe of the polynucleotide encodingPTAM, and improper or unexpected hybridization to allelic variants, witha locus other than the normal chromosomal locus for the polynucleotidesequence encoding PTAM. The encoded protein may also be “altered,” andmay contain deletions, insertions, or substitutions of amino acidresidues which produce a silent change and result in a functionallyequivalent PTAM. Deliberate amino acid substitutions may be made on thebasis of similarity in polarity, charge, solubility, hydrophobicity,hydrophilicity, and/or the amphipathic nature of the residues, as longas the biological or immunological activity of PTAM is retained. Forexample, negatively charged amino acids may include aspartic acid andglutamic acid, positively charged amino acids may include lysine andarginine, and amino acids with uncharged polar head groups havingsimilar hydrophilicity values may include leucine, isoleucine, andvaline; glycine and alanine; asparagine and glutamine; serine andthreonine; and phenylalanine and tyrosine.

The terms “amino acid” or “amino acid sequence” refer to anoligopeptide, peptide, polypeptide, or protein sequence, or a fragmentof any of these, and to naturally occurring or synthetic molecules. Inthis context, “fragments,” “immunogenic fragments,” or “antigenicfragments” refer to fragments of PTAM which are preferably at least 5 toabout 15 amino acids in length, most preferably at least 14 amino acids,and which retain some biological activity or immunological activity ofPTAM. Where “amino acid sequence” is recited to refer to an amino acidsequence of a naturally occurring protein molecule, “amino acidsequence” and like terms are not meant to limit the amino acid sequenceto the complete native amino acid sequence associated with the recitedprotein molecule.

“Amplification” relates to the production of additional copies of anucleic acid sequence. Amplification is generally carried out usingpolymerase chain reaction (PCR) technologies well known in the art.

The term “antagonist” refers to a molecule which, when bound to PTAM,decreases the amount or the duration of the effect of the biological orimmunological activity of PTAM. Antagonists may include proteins,nucleic acids, carbohydrates, antibodies, or any other molecules whichdecrease the effect of PTAM.

The term “antibody” refers to intact molecules as well as to fragmentsthereof, such as Fab, F(ab′)₂, and Fv fragments, which are capable ofbinding the epitopic determinant. Antibodies that bind PTAM polypeptidescan be prepared using intact polypeptides or using fragments containingsmall peptides of interest as the immunizing antigen. The polypeptide oroligopeptide used to immunize an animal (e.g., a mouse, a rat, or arabbit) can be derived from the translation of RNA, or synthesizedchemically, and can be conjugated to a carrier protein if desired.Commonly used carriers that are chemically coupled to peptides includebovine serum albumin, thyroglobulin, and keyhole limpet hemocyanin(KLH). The coupled peptide is then used to immunize the animal.

The term “antigenic determinant” refers to that fragment of a molecule(i.e., an epitope) that makes contact with a particular antibody. When aprotein or a fragment of a protein is used to immunize a host animal,numerous regions of the protein may induce the production of antibodieswhich bind specifically to antigenic determinants (given regions orthree-dimensional structures on the protein). An antigenic determinantmay compete with the intact antigen (i.e., the immunogen used to elicitthe immune response) for binding to an antibody.

The term “antisense” refers to any composition containing a nucleic acidsequence which is complementary to the “sense” strand of a specificnucleic acid sequence. Antisense molecules may be produced by any methodincluding synthesis or transcription. Once introduced into a cell, thecomplementary nucleotides combine with natural sequences produced by thecell to form duplexes and to block either transcription or translation.The designation “negative” can refer to the antisense strand, and thedesignation “positive” can refer to the sense strand.

The term “biologically active,” refers to a protein having structural,regulatory, or biochemical functions of a naturally occurring molecule.Likewise, “immunologically active” refers to the capability of thenatural, recombinant, or synthetic PTAM, or of any oligopeptide thereof,to induce a specific immune response in appropriate animals or cells andto bind with specific antibodies.

The terms “complementary” or “complementarity” refer to the naturalbinding of polynucleotides by base pairing. For example, the sequence“5′ A-G-T 3′” bonds to the complementary sequence “3′ T-C-A 5′.”Complementarity between two single-stranded molecules may be “partial,”such that only some of the nucleic acids bind, or it may be “complete,”such that total complementarity exists between the single strandedmolecules. The degree of complementarity between nucleic acid strandshas significant effects on the efficiency and strength of thehybridization between the nucleic acid strands. This is of particularimportance in amplification reactions, which depend upon binding betweennucleic acids strands, and in the design and use of peptide nucleic acid(PNA) molecules.

A “composition comprising a given polynucleotide sequence” or a“composition comprising a given amino acid sequence” refer broadly toany composition containing the given polynucleotide or amino acidsequence. The composition may comprise a dry formulation or an aqueoussolution. Compositions comprising polynucleotide sequences encoding PTAMor fragments of PTAM may be employed as hybridization probes. The probesmay be stored in freeze-dried form and may be associated with astabilizing agent such as a carbohydrate. In hybridizations, the probemay be deployed in an aqueous solution containing salts (e.g., NaCl),detergents (e.g., sodium dodecyl sulfate; SDS), and other components(e.g., Denhardt's solution, dry milk, salmon sperm DNA, etc.).

“Consensus sequence”refers to a nucleic acid sequence which has beenresequenced to resolve uncalled bases, extended using XL-PCR kit(Perkin-Elmer, Norwalk CT) in the 5′ and/or the 3′ direction, andresequenced, or which has been assembled from the overlapping sequencesof more than one Incyte Clone using a computer program for fragmentassembly, such as the GELVIEW Fragment Assembly system (GCG, MadisonWis.). Some sequences have been both extended and assembled to producethe consensus sequence.

The term “correlates with expression of a polynucleotide” indicates thatthe detection of the presence of nucleic acids, the same or related to anucleic acid sequence encoding PTAM, by northern analysis is indicativeof the presence of nucleic acids encoding PTAM in a sample; and therebycorrelates with expression of the transcript from the polynucleotideencoding PTAM.

A “deletion”refers to a change in the amino acid or nucleotide sequencethat results in the absence of one or more amino acid residues ornucleotides.

The term “derivative” refers to the chemical modification of apolypeptide sequence, or a polynucleotide sequence. Chemicalmodifications of a polynucleotide sequence can include, for example,replacement of hydrogen by an alkyl, acyl, or amino group. A derivativepolynucleotide encodes a polypeptide which retains at least onebiological or immunological function of the natural molecule. Aderivative polypeptide is one modified by glycosylation, pegylation, orany similar process that retains at least one biological orimmunological function of the polypeptide from which it was derived.

The term “similarity” refers to a degree of complementarity. There maybe partial similarity or complete similarity. The word “identity” maysubstitute for the word “similarity.” A partially complementary sequencethat at least partially inhibits an identical sequence from hybridizingto a target nucleic acid is referred to as “substantially similar.” Theinhibition of hybridization of the completely complementary sequence tothe target sequence may be examined using a hybridization assay(Southern or northern blot, solution hybridization, and the like) underconditions of reduced stringency. A substantially similar sequence orhybridization probe will compete for and inhibit the binding of acompletely similar (identical) sequence to the target sequence underconditions of reduced stringency. This is not to say that conditions ofreduced stringency are such that non-specific binding is permitted, asreduced stringency conditions require that the binding of two sequencesto one another be a specific (i.e., a selective) interaction. Theabsence of non-specific binding may be tested by the use of a secondtarget sequence which lacks even a partial degree of complementarity(e.g., less than about 30% similarity or identity). In the absence ofnon-specific binding, the substantially similar sequence or probe willnot hybridize to the second non-complementary target sequence.

The phrases “percent identity” or “% identity” refer to the percentageof sequence similarity found in a comparison of two or more amino acidor nucleic acid sequences. Percent identity can be determinedelectronically, e.g., by using the MEGALIGN program (DNASTAR, MadisonWis.). The MEGALIGN program can create alignments between two or moresequences according to different methods, e.g., the clustal method.(See, e.g., Higgins, D. G. and P. M. Sharp (1988) Gene 73:237-244.) Theclustal algorithm groups sequences into clusters by examining thedistances between all pairs. The clusters are aligned pairwise and thenin groups. The percentage similarity between two amino acid sequences,e.g., sequence A and sequence B; is calculated by dividing the length ofsequence A, minus the number of gap residues in sequence A, minus thenumber of gap residues in sequence B, into the sum of the residuematches between sequence A and sequence B, times one hundred. Gaps oflow or of no similarity between the two amino acid sequences-are notincluded in determining percentage similarity. Percent identity betweennucleic acid sequences can also be counted or calculated by othermethods known in the art, e.g., the Jotun Hein method. (See, e.g., Hein,J. (1990) Methods Enzymol. 183:626-645.) Identity between sequences canalso be determined by other methods known in the art, e.g., by varyinghybridization conditions.

“Human artificial chromosomes” (HACs) are linear microchromosomes whichmay contain DNA sequences of about 6 kb to 10 Mb in size, and whichcontain all of the elements required for stable mitotic chromosomesegregation and maintenance.

The term “humanized antibody” refers to antibody molecules in which theamino acid sequence in the non-antigen binding regions has been alteredso that the antibody more closely resembles a human antibody, and stillretains its original binding ability.

“Hybridization” refers to any process by which a strand of nucleic acidbinds with a complementary strand through base pairing.

The term “hybridization complex” refers to a complex formed between twonucleic acid sequences by virtue of the formation of hydrogen bondsbetween complementary bases. A hybridization complex may be formed insolution (e.g., C₀t or R₀t analysis) or formed between one nucleic acidsequence present in solution and another nucleic acid sequenceimmobilized on a solid support (e.g., paper, membranes, filters, chips,pins or glass slides, or any other appropriate substrate to which cellsor their nucleic acids have been fixed).

The words “insertion” or “addition” refer to changes in an amino acid ornucleotide sequence resulting in the addition of one or more amino acidresidues or nucleotides, respectively, to the sequence found in thenaturally occurring molecule.

“Immune response” can refer to conditions associated with inflammation,trauma, immune disorders, or infectious or genetic disease, etc. Theseconditions can be characterized by expression of various factors, e.g.,cytokines, chemokines, and other signaling molecules, which may affectcellular and systemic defense systems.

The term “microarray” refers to an arrangement of distinctpolynucleotides on a substrate.

The terms “element” or “array element” in a microarray context, refer tohybridizable polynucleotides arranged on the surface of a substrate.

The term “modulate” refers to a change in the activity of PTAM. Forexample, modulation may cause an increase or a decrease in proteinactivity, binding characteristics, or any other biological, functional,or immunological properties of PTAM.

The phrases “nucleic acid” or “nucleic acid sequence,” as used herein,refer to a nucleotide, oligonucleotide, polynucleotide, or any fragmentthereof. These phrases also refer to DNA or RNA of genomic or syntheticorigin which may be single-stranded or double-stranded and may representthe sense or the antisense strand, to peptide nucleic acid (PNA), or toany DNA-like or RNA-like material. In this context, “fragments” refersto those nucleic acid sequences which comprise a region of uniquepolynucleotide sequence that specifically identifies SEQ ID NO:9-16, forexample, as distinct from any other sequence in the same genome. Forexample, a fragment of SEQ ID NO:9-16 is useful in hybridization andamplification technologies and in analogous methods that distinguish SEQID NO:9-16 from related polynucleotide sequences. A fragment of SEQ IDNO:9-16 is at least about 15-20 nucleotides in length. The preciselength of the fragment of SEQ ID NO:9-16 and the region of SEQ IDNO:9-16 to which the fragment corresponds are routinely determinable byone of ordinary skill in the art based on the intended purpose for thefragment. In some cases, a fragment, when translated, would producepolypeptides retaining some functional characteristic, e.g.,antigenicity, or structural domain characteristic, e.g., ATP-bindingsite, of the full-length polypeptide.

The terms “operably associated” or “operably linked” refer tofunctionally related nucleic acid sequences. A promoter is operablyassociated or operably linked with a coding sequence if the promotercontrols the translation of the encoded polypeptide. While operablyassociated or operably linked nucleic acid sequences can be contiguousand in the same reading frame, certain genetic elements, e.g., repressorgenes, are not contiguously linked to the sequence encoding thepolypeptide but still bind to operator sequences that control expressionof the polypeptide.

The term “oligonucleotide” refers to a nucleic acid sequence of at leastabout 6 nucleotides to 60 nucleotides, preferably about 15 to 30nucleotides, and most preferably about 20 to 25 nucleotides, which canbe used in PCR amplification or in a hybridization assay or microarray.“Oligonucleotide” is substantially equivalent to the terms “amplimer,”“primer,” “oligomer,” and “probe,” as these terms are commonly definedin the art.

“Peptide nucleic acid” (PNA) refers to an antisense molecule oranti-gene agent which comprises an oligonucleotide of at least about 5nucleotides in length linked to a peptide backbone of amino acidresidues ending in lysine. The terminal lysine confers solubility to thecomposition. PNAs preferentially bind complementary single stranded DNAor RNA and stop transcript elongation, and may be pegylated to extendtheir lifespan in the cell.

The term “sample” is used in its broadest sense. A sample suspected ofcontaining nucleic acids encoding PTAM, or fragments thereof, or PTAMitself, may comprise a bodily fluid; an extract from a cell, chromosome,organelle, or membrane isolated from a cell; a cell; genomic DNA, RNA,or cDNA, in solution or bound to a substrate; a tissue; a tissue print;etc.

The terms “specific binding” or “specifically binding” refer to thatinteraction between a protein or peptide and an agonist, an antibody, oran antagonist. The interaction is dependent upon the presence of aparticular structure of the protein, e.g., the antigenic determinant orepitope, recognized by the binding molecule. For example, if an antibodyis specific for epitope “A,” the presence of a polypeptide containingthe epitope A, or the presence of free unlabeled A, in a reactioncontaining free labeled A and the antibody will reduce the amount oflabeled A that binds to the antibody.

The term “stringent conditions” refers to conditions which permithybridization between polynucleotides and the claimed polynucleotides.Stringent conditions can be defined by salt concentration, theconcentration of organic solvent, e.g., formamide, temperature, andother conditions well known in the art. In particular, stringency can beincreased by reducing the concentration of salt, increasing theconcentration of formamide, or raising the hybridization temperature.

The term “substantially purified” refers to nucleic acid or amino acidsequences that are removed from their natural environment and areisolated or separated, and are at least about 60% free, preferably about75% free, and most preferably about 90% free from other components withwhich they are naturally associated.

A “substitution” refers to the replacement of one or more amino acids ornucleotides by different amino acids or nucleotides, respectively.

“Substrate” refers to any suitable rigid or semi-rigid support includingmembranes, filters, chips, slides, wafers, fibers, magnetic ornonmagnetic beads, gels, tubing, plates, polymers, microparticles andcapillaries. The substrate can have a variety of surface forms, such aswells, trenches, pins, channels and pores, to which polynucleotides orpolypeptides are bound.

“Transformation” describes a process by which exogenous DNA enters andchanges a recipient cell. Transformation may occur under natural orartificial conditions according to various methods well known in theart, and may rely on any known method for the insertion of foreignnucleic acid sequences into a prokaryotic or eukaryotic host cell. Themethod for transformation is selected based on the type of host cellbeing transformed and may include, but is not limited to, viralinfection, electroporation, heat shock, lipofection, and particlebombardment. The term “transformed” cells includes stably transformedcells in which the inserted DNA is capable of replication either as anautonomously replicating plasmid or as part of the host chromosome, aswell as transiently transformed cells which express the inserted DNA orRNA for limited periods of time.

A “variant” of PTAM polypeptides refers to an amino acid sequence thatis altered by one or more amino acid residues. The variant may have“conservative” changes, wherein a substituted amino acid has similarstructural or chemical properties (e.g., replacement of leucine withisoleucine). More rarely, a variant may have “nonconservative” changes(e.g., replacement of glycine with tryptophan). Analogous minorvariations may also include amino acid deletions or insertions, or both.Guidance in determining which amino acid residues may be substituted,inserted, or deleted without abolishing biological or immunologicalactivity may be found using computer programs well known in the art, forexample, LASERGENE software (DNASTAR).

The term “variant,” when used in the context of a polynucleotidesequence, may encompass a polynucleotide sequence related to PTAM. Thisdefinition may also include, for example, “allelic” (as defined above),“splice,” “species,” or “polymorphic” variants. A splice variant mayhave significant identity to a reference molecule, but will generallyhave a greater or lesser number of polynucleotides due to alternatesplicing of exons during mRNA processing. The corresponding polypeptidemay possess additional functional domains or an absence of domains.Species variants are polynucleotide sequences that vary from one speciesto another. The resulting polypeptides generally will have significantamino acid identity relative to each other. A polymorphic variant is avariation in the polynucleotide sequence of a particular gene betweenindividuals of a given species. Polymorphic variants also may encompass“single nucleotide polymorphisms” (SNPs) in which the polynucleotidesequence varies by one base. The presence of SNPs may be indicative of,for example, a certain population, a disease state, or a propensity fora disease state.

The Invention

The invention is based on the discovery of new human proteintransport-associated molecules (PTAM), the polynucleotides encodingPTAM, and the use of these compositions for the diagnosis, treatment, orprevention of cell proliferative and secretory disorders.

Table 1 lists the Incyte Clones used to derive full length nucleotidesequences encoding PTAM. Columns 1 and 2 show the sequenceidentification numbers (SEQ ID NO) of the amino acid and nucleic acidsequences, respectively. Column 3 shows the Clone ID of the Incyte Clonein which nucleic acids encoding each PTAM were first identified, andcolumn 4, the cDNA libraries from which these clones were isolated.Column 5 shows Incyte clones, their corresponding cDNA libraries, andshotgun sequences useful as fragments in hybridization technologies, andwhich are part of the consensus nucleotide sequence of each PTAM.

The columns of Table 2 show various properties of the polypeptides ofthe invention: column 1 references the SEQ ID NO; column 2 shows thenumber of amino acid residues in each polypeptide; column 3, potentialphosphorylation sites; column 4, potential glycosylation sites; column5, the amino acid residues comprising signature sequences and motifs;column 6, the identity of each protein; and column 7, analytical methodsused to identify each protein through sequence homology and proteinmotifs.

The columns of Table 3 show the tissue-specificity anddisease-association of nucleotide sequences encoding PTAM. The firstcolumn of Table 3 lists the polynucleotide sequence identifiers. Thesecond column lists tissue categories which express PTAM as a fractionof total tissue categories expressing PTAM. The third column lists thedisease classes associated with those tissues expressing PTAM. Thefourth column lists the vectors used to subclone the cDNA library.

The following represent unique fragments of the nucleotide sequencesencoding PTAM: the fragment of SEQ ID NO:9 from about nucleotide 1324 toabout nucleotide 1422; the fragment of SEQ ID NO:10 from aboutnucleotide 455 to about nucleotide 499; the fragment of SEQ ID NO:11from about nucleotide 101 to about nucleotide 145; the fragment of SEQID NO:12 from about nucleotide 178 to about nucleotide 240; the fragmentof SEQ ID NO:13 from about nucleotide 543 to about nucleotide 590; thefragment of SEQ ID NO:14 from about nucleotide 525 to about nucleotide584; the fragment of SEQ ID NO:15 from about nucleotide 371 to aboutnucleotide 433; and the fragment of SEQ ID NO:16 from about nucleotide86 to about nucleotide 145.

The invention also encompasses PTAM variants. A preferred PTAM variantis one which has at least about 80%, more preferably at least about 90%,and most preferably at least about 95% amino acid sequence identity tothe PTAM amino acid sequence, and which contains at least one functionalor structural characteristic of PTAM.

The invention also encompasses polynucleotides which encode PTAM. In aparticular embodiment, the invention encompasses a polynucleotidesequence comprising a sequence selected from the group consisting of SEQID NO:9-16, which encodes PTAM.

The invention also encompasses a variant of a polynucleotide sequenceencoding PTAM. In particular, such a variant polynucleotide sequencewill have at least about 70%, more preferably at least about 85%, andmost preferably at least about 95% polynucleotide sequence identity tothe polynucleotide sequence encoding PTAM. A particular aspect of theinvention encompasses a variant of a polynucleotide sequence comprisinga sequence selected from the group consisting of SEQ ID NO:9-16 whichhas at least about 70%, more preferably at least about 85%, and mostpreferably at least about 95% polynucleotide sequence identity to anucleic acid sequence selected from the group consisting of SEQ IDNO:9-16. Any one of the polynucleotide variants described above canencode an amino acid sequence which contains at least one functional orstructural characteristic of PTAM.

It will be appreciated by those skilled in the art that as a result ofthe degeneracy of the genetic code, a multitude of polynucleotidesequences encoding PTAM, some bearing minimal similarity to thepolynucleotide sequences of any known and naturally occurring gene, maybe produced. Thus, the invention contemplates each and every possiblevariation of polynucleotide sequence that could be made by selectingcombinations based on possible codon choices. These combinations aremade in accordance with the standard triplet genetic code as applied tothe polynucleotide sequence of naturally occurring PTAM, and all suchvariations are to be considered as being specifically disclosed.

Although nucleotide sequences which encode PTAM and its variants arepreferably capable of hybridizing to the nucleotide sequence of thenaturally occurring PTAM under appropriately selected conditions ofstringency, it may be advantageous to produce nucleotide sequencesencoding PTAM or its derivatives possessing a substantially differentcodon usage, e.g., inclusion of non-naturally occurring codons. Codonsmay be selected to increase the rate at which expression of the peptideoccurs in a particular prokaryotic or eukaryotic host in accordance withthe frequency with which particular codons are utilized by the host.Other reasons for substantially altering the nucleotide sequenceencoding PTAM and its derivatives without altering the encoded aminoacid sequences include the production of RNA transcripts having moredesirable properties, such as a greater half-life, than transcriptsproduced from the naturally occurring sequence.

The invention also encompasses production of DNA sequences which encodePTAM and PTAM derivatives, or fragments thereof, entirely by syntheticchemistry. After production, the synthetic sequence may be inserted intoany of the many available expression vectors and cell systems usingreagents well known in the art. Moreover, synthetic chemistry may beused to introduce mutations into a sequence encoding PTAM or anyfragment thereof.

Also encompassed by the invention are polynucleotide sequences that arecapable of hybridizing to the claimed polynucleotide sequences, and, inparticular, to those shown in SEQ ID NO:9-16 and fragments thereof undervarious conditions of stringency. (See, e.g., Wahl, G. M. and S. L.Berger (1987) Methods Enzymol. 152:399-407; Kimmel, A. R. (1987) MethodsEnzymol. 152:507-511.) For example, stringent salt concentration willordinarily be less than about 750 mM NaCl and 75 mM trisodium citrate,preferably less than about 500 mM NaCl and 50 mM trisodium citrate, andmost preferably less than about 250 mM NaCl and 25 mM trisodium citrate.Low stringency hybridization can be obtained in the absence of organicsolvent, e.g., formamide, while high stringency hybridization can beobtained in the presence of at least about 35% formamide, and mostpreferably at least about 50% formamide. Stringent temperatureconditions will ordinarily include temperatures of at least about 30°C., more preferably of at least about 37° C., and most preferably of atleast about 42° C. Varying additional parameters, such as hybridizationtime, the concentration of detergent, e.g., sodium dodecyl sulfate(SDS); and the inclusion or exclusion of carrier DNA, are well known tothose skilled in the art. Various levels of stringency are accomplishedby combining these various conditions as needed. In a preferredembodiment, hybridization will occur at 30° C. in 750 mM NaCl, 75 mMtrisodium citrate, and 1% SDS. In a more preferred embodiment,hybridization will occur at 37° C. in 500 mM NaCl, 50 mM trisodiumcitrate, 1% SDS, 35% formamide, and 100 μg/ml denatured salmon sperm DNA(ssDNA). In a most preferred embodiment, hybridization will occur at 42°C. in 250 mM NaCl, 25 mM trisodium citrate, 1% SDS, 50% formamide, and200 μg/ml ssDNA. Useful variations on these conditions will be readilyapparent to those skilled in the art.

The washing steps which follow hybridization can also vary instringency. Wash stringency conditions can be defined by saltconcentration and by temperature. As above, wash stringency can beincreased by decreasing salt concentration or by increasing temperature.For example, stringent salt concentration for the wash steps willpreferably be less than about 30 mM NaCl and 3 mM trisodium citrate, andmost preferably less than about 15 mM NaCl and 1.5 mM trisodium citrate.Stringent temperature conditions for the wash steps will ordinarilyinclude temperature of at least about 25° C., more preferably of atleast about 42° C., and most preferably of at least about 68° C. In apreferred embodiment, wash steps will occur at 25° C. in 30 mM NaCl, 3mM trisodium citrate, and 0.1% SD S. In a more preferred embodiment,wash steps will occur at 42° C. in 15 mM NaCl, 1.5 mM trisodium citrate,and 0.1% SDS. In a most preferred embodiment, wash steps will occur at68° C. in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. Additionalvariations on these conditions will be readily apparent to those skilledin the art.

Methods for DNA sequencing are well known in the art and may be used topractice any of the embodiments of the invention. The methods may employsuch enzymes as the Klenow fragment of DNA polymerase I, SEQUENASE (USBiochemical, Cleveland Ohio), TAQ polymerase (Perkin-Elmer),thermostable T7 polymerase (Amersham Pharmacia Biotech, PiscatawayN.J.), or combinations of polymerases and proofreading exonucleases suchas those found in the ELONGASE amplification system (Life Technologies,Gaithersburg Md.). Preferably, sequence preparation is automated withmachines such as the Hamilton MICROLAB 2200 (Hamilton, Reno Nev.),PELTIER THERMAL CYCLER 200 (PTC200; MJ Research, Watertown Mass.) andthe ABI CATALYST 800 PCR reaction machine (Perkin-Elmer). Sequencing isthen carried out using either ABI 373 or 377 DNA Sequencing Systems(Perkin-Elmer) or the MEGABACE capillary electrophoresis system(Molecular Dynamics, Sunnyvale Calif.). The resulting sequences areanalyzed using a variety of algorithms which are well known in the art.(See, e.g., Ausubel, F. M. (1997) Short Protocols in Molecular Biology,John Wiley & Sons, New York N.Y., unit 7.7; Meyers, R. A. (1995)Molecular Biology and Biotechnology, Wiley VCH, New York N.Y., pp.856-853.)

The nucleic acid sequences encoding PTAM may be extended utilizing apartial nucleotide sequence and employing various PCR-based methodsknown in the art to detect upstream sequences, such as promoters andregulatory elements. For example, one method which may be employed,restriction-site PCR, uses universal and nested primers to amplifyunknown sequence from genomic DNA within a cloning vector. (See, e.g.,Sarkar, G. (1993) PCR Methods Applic. 2:318-322.) Another method,inverse PCR, uses primers that extend in divergent directions to amplifyunknown sequence from a circularized template. The template is derivedfrom restriction fragments comprising a known genomic locus andsurrounding sequences. (See, e.g., Triglia, T. et al. (1988) NucleicAcids Res. 16:8186.) A third method, capture PCR, involves PCRamplification of DNA fragments adjacent to known sequences in human andyeast artificial chromosome DNA. (See, e.g., Lagerstrom, M. et al.(1991) PCR Methods Applic. 111-119.) In this method, multiplerestriction enzyme digestions and ligations may be used to insert anengineered double-stranded sequence into a region of unknown sequencebefore performing PCR. Other methods which may be used to retrieveunknown sequences are known in the art. (See, e.g., Parker, J. D. et al.(1991) Nucleic Acids Res. 19:3055-306.) Additionally, one may use PCR,nested primers, and PROMOTERFINDER libraries (Clontech, Palo AltoCalif.) to walk genomic DNA. This procedure avoids the need to screenlibraries and is useful in finding intron/exon junctions. For all,PCR-based methods, primers may be designed using commercially availablesoftware, such as OLIGO 4.06 Primer Analysis software (NationalBiosciences, Plymouth Minn.) or another appropriate program, to be about22 to 30 nucleotides in length, to have a GC content of about 50% ormore, and to anneal to the template at temperatures of about 68° C. to72° C.

When screening for full-length cDNAs, it is preferable to use librariesthat have been size-selected to include larger cDNAs. In addition,random-primed libraries, which often include sequences containing the 5′regions of genes, are preferable for situations in which an oligo d(T)library does not yield a full-length cDNA. Genomic libraries may beuseful for extension of sequence into 5′ non-transcribed regulatoryregions.

Capillary electrophoresis systems which are commercially available maybe used to analyze the size or confirm the nucleotide sequence ofsequencing or PCR products. In particular, capillary sequencing mayemploy flowable polymers for electrophoretic separation, four differentnucleotide-specific, laser-stimulated fluorescent dyes, and a chargecoupled device camera for detection of the emitted wavelengths.Output/light intensity may be converted to electrical signal usingappropriate software (e.g., GENOTYPER and SEQUENCE NAVIGATOR,Perkin-Elmer), and the entire process from loading of samples tocomputer analysis and electronic data display may be computercontrolled. Capillary electrophoresis is especially preferable forsequencing small DNA fragments which may be present in limited amountsin a particular sample.

In another embodiment of the invention, polynucleotide sequences orfragments thereof which encode PTAM may be cloned in recombinant DNAmolecules that direct expression of PTAM, or fragments or functionalequivalents thereof, in appropriate host cells. Due to the inherentdegeneracy of the genetic code, other DNA sequences which encodesubstantially the same or a functionally equivalent amino acid sequencemay be produced and used to express PTAM.

The nucleotide sequences of the present invention can be engineeredusing methods generally known in the art in order to alter PTAM-encodingsequences for a variety of purposes including, but not limited to,modification of the cloning, processing, and/or expression of the geneproduct. DNA shuffling by random fragmentation and PCR reassembly ofgene fragments and synthetic oligonucleotides may be used to engineerthe nucleotide sequences. For example, oligonucleotide-mediatedsite-directed mutagenesis may be used to introduce mutations that createnew restriction sites, alter glycosylation patterns, change codonpreference, produce splice variants, and so forth.

In another embodiment, sequences encoding PTAM may be synthesized, inwhole or in part, using chemical methods well known in the art. (See,e.g., Caruthers, M. H. et al. (1980) Nucl. Acids Res. Symp. Ser.215-223, and Horn, T. et al. (1980) Nucl. Acids Res. Symp. Ser.225-232.) Alternatively, PTAM itself or a fragment thereof may besynthesized using chemical methods. For example, peptide synthesis canbe performed using various solid-phase techniques. (See, e.g., Roberge,J. Y. et al. (1995) Science 269:202-204.) Automated synthesis may beachieved using the ABI 43 IA Peptide Synthesizer (Perkin-Elmer).Additionally, the amino acid sequence of PTAM, or any part thereof, maybe altered during direct synthesis and/or combined with sequences fromother proteins, or any part thereof, to produce a variant polypeptide.

The peptide may be substantially purified by preparative highperformance liquid chromatography. (See, e.g, Chiez, R. M. and F. Z.Regnier (1990) Methods Enzymol. 182:392-421.) The composition of thesynthetic peptides may be confirmed by amino acid analysis or bysequencing. (See, e.g., Creighton, T. (1984) Proteins, Structures andMolecular Properties, W. H. Freeman, New York N.Y.)

In order to express a biologically active PTAM, the nucleotide sequencesencoding PTAM or derivatives thereof may be inserted into an appropriateexpression vector, i.e., a vector which contains the necessary elementsfor transcriptional and translational control of the inserted codingsequence in a suitable host. These elements include regulatorysequences, such as enhancers, constitutive and inducible promoters, and5′ and 3′ untranslated regions in the vector and in polynucleotidesequences encoding PTAM. Such elements may vary in their strength andspecificity. Specific initiation signals may also be used to achievemore efficient translation of sequences encoding PTAM. Such signalsinclude the ATG initiation codon and adjacent sequences, e.g. the Kozaksequence. In cases where sequences encoding PTAM and its initiationcodon and upstream regulatory sequences are inserted into theappropriate expression vector, no additional transcriptional ortranslational control signals may be needed. However, in cases whereonly coding sequence, or a fragment thereof, is inserted, exogenoustranslational control signals including an in-frame ATG initiation codonshould be provided by the vector. Exogenous translational elements andinitiation codons may be of various origins, both natural and synthetic.The efficiency of expression may be enhanced by the inclusion ofenhancers appropriate for the particular host cell system used. (See,e.g., Scharf, D. et al. (1994) Results Probl. Cell Differ. 20:125-162.)

Methods which are well known to those skilled in the art may be used toconstruct expression vectors containing sequences encoding PTAM andappropriate transcriptional and translational control elements. Thesemethods include in vitro recombinant DNA techniques, synthetictechniques, and in vivo genetic recombination. (See, e.g., Sambrook, J.et al. (1989) Molecular Cloning, A Laboratory Manual, Cold Spring HarborPress, Plainview N.Y., ch. 4, 8, and 16-17; Ausubel, F. M. et al. (1995)Current Protocols in Molecular Biology, John Wiley & Sons, New YorkN.Y., ch. 9, 13, and 16.)

A variety of expression vector/host systems may be utilized to containand express sequences encoding PTAM. These include, but are not limitedto, microorganisms such as bacteria transformed with recombinantbacteriophage, plasmid, or cosmid DNA expression vectors; yeasttransformed with yeast expression vectors; insect cell systems infectedwith viral expression vectors (e.g., baculovirus); plant cell systemstransformed with viral expression vectors (e.g., cauliflower mosaicvirus, CaMV, or tobacco mosaic virus,TMV) or with bacterial expressionvectors (e.g., Ti or pBR322 plasmids); or animal cell systems. Theinvention is not limited by the host cell employed.

In bacterial systems, a number of cloning and expression vectors may beselected depending upon the use intended for polynucleotide sequencesencoding PTAM. For example, routine cloning, subcloning, and propagationof polynucleotide sequences encoding PTAM can be achieved using amultifunctional E. coli vector such as PBLUESCRIPT (Stratagene, La JollaCalif.) or PSPORT1 plasmid (Life Technologies). Ligation of sequencesencoding PTAM into the vector's multiple cloning site disrupts the lacZgene, allowing a calorimetric screening procedure for identification oftransformed bacteria containing recombinant molecules. In addition,these vectors may be useful for in vitro transcription, dideoxysequencing, single strand rescue with helper phage, and creation ofnested deletions in the cloned sequence. (See, e.g., Van Heeke, G. andS. M. Schuster (1989) J. Biol. Chem. 264:5503-5509.) When largequantities of PTAM are needed, e.g. for the production of antibodies,vectors which direct high level expression of PTAM may be used. Forexample, vectors containing the strong, inducible T5 or T7 bacteriophagepromoter may be used.

Yeast expression systems may be used for production of PTAM. A number ofvectors containing constitutive or inducible promoters, such as alphafactor, alcohol oxidase, and PGH, may be used in the yeast Saccharomycescerevisiae or Pichia pastoris. In addition, such vectors direct eitherthe secretion or intracellular retention of expressed proteins andenable integration of foreign sequences into the host genome for stablepropagation. (See, e.g.; Ausubel, 1995, supra; Grant et al. (1987)Methods Enzymol. 153:516-54; and Scorer, C. A. et al. (1994)Bio/Technology 12:181-184.)

Plant systems may also be used for expression of PTAM. Transcription ofsequences encoding PTAM may be driven viral promoters, e.g., the 35S and19S promoters of CaMV used alone or in combination with the omega leadersequence from TMV. (Takamatsu, N. (1987) EMBO J. 6:307-311.)Alternatively, plant promoters such as the small subunit of RUBISCO orheat shock promoters may be used. (See, e.g., Coruzzi, G. et al. (1984)EMBO J. 3:1671-1680; Broglie, R. et al. (1984) Science 224:838-843; andWinter, J. et al. (1991) Results Probl. Cell Differ. 17:85-105.) Theseconstructs can be introduced into plant cells by direct DNAtransformation or pathogen-mediated transfection. (See, e.g., The McGrawHill Yearbook of Science and Technology (1992) McGraw Hill; New YorkN.Y., pp. 191-196.)

In mammalian cells, a number of viral-based expression systems may beutilized. In cases where an adenovirus is used as an expression vector,sequences encoding PTAM may be ligated into an adenovirustranscription/translation complex consisting of the late promoter andtripartite leader sequence. Insertion in a non-essential E1 or E3 regionof the viral genome may be used to obtain infective virus whichexpresses PTAM in host cells. (See, e.g., Logan, J. and T. Shenk (1984)Proc. Natl. Acad. Sci. 81:3655-3659.) In addition, transcriptionenhancers, such as the Rous sarcoma virus (RSV) enhancer, may be used toincrease expression in mammalian host cells. SV40 or EBV-based vectorsmay also be used for high-level protein expression.

Human artificial chromosomes (HACs) may also be employed to deliverlarger fragments of DNA than can be contained in and expressed from aplasmid. HACs of about 6 kb to 10 Mb are constructed and delivered viaconventional delivery methods (liposomes, polycationic amino polymers,or vesicles) for therapeutic purposes. (See, e.g., Harrington, J. J. etal. (1997) Nat Genet. 15:345-355.)

For long term production of recombinant proteins in mammalian systems,stable expression of PTAM in cell lines is preferred. For example,sequences encoding PTAM can be transformed into cell lines usingexpression vectors which may contain viral origins of replication and/orendogenous expression elements and a selectable marker gene on the sameor on a separate vector. Following the introduction of the vector, cellsmay be allowed to grow for about 1 to 2 days in enriched media beforebeing switched to selective media. The purpose of the selectable markeris to confer resistance to a selective agent, and its presence allowsgrowth and recovery of cells which successfully express the introducedsequences. Resistant clones of stably transformed cells may bepropagated using tissue culture techniques appropriate to the cell type.

Any number of selection systems may be used to recover transformed celllines. These include, but are not limited to, the herpes simplex virusthymidine kinase and adenine phosphoribosyltransferase genes, for use intk or apr cells, respectively. (See, e.g., Wigler, M. et al. (1977) Cell11:223-232; Lowy, I. et al. (1980) Cell 22:817-823.) Also,antimetabolite, antibiotic, or herbicide resistance can be used as thebasis for selection. For example, dhfr confers resistance tomethotrexate; neo confers resistance to the aminoglycosides neomycin andG-418; and als or put confer resistance to chlorsulfuron andphosphinotricin acetyltransferase, respectively. (See, e.g., Wigler, M.et al. (1980) Proc. Natl. Acad. Sci. 77:3567-3570; Colbere-Garapin, F.et al. (1981) J. Mol. Biol. 150:1-14) Additional selectable genes havebeen described, e.g., trpB and hisD, which alter cellular requirementsfor metabolites. (See, e.g., Hartman, S. C. and R. C. Mulligan (1988)Proc. Natl. Acad. Sci. 85:8047-8051.) Visible markers, e.g.,anthocyanins, green fluorescent proteins (GFP; Clontech), βglucuronidase and its substrate β-glucuronide, or luciferase and itssubstrate luciferin may be used. These markers can be used not only toidentify transform ants, but also to quantify the amount of transient orstable protein expression attributable to a specific vector system.(See, e.g., Rhodes, C. A. (1995) Methods Mol. Biol. 55:121-131.)

Although the presence/absence of marker gene expression suggests thatthe gene of interest is also present, the presence and expression of thegene may need to be confirmed. For example, if the sequence encodingPTAM is inserted within a marker gene sequence, transformed cellscontaining sequences encoding PTAM can be identified by the absence ofmarker gene function. Alternatively, a marker gene can be placed intandem with a sequence encoding PTAM under the control of a singlepromoter. Expression of the marker gene in response to induction orselection usually indicates expression of the tandem gene as well.

In general, host cells that contain the nucleic acid sequence encodingPTAM and that express PTAM may be identified by a variety of proceduresknown to those of skill in the art. These procedures include, but arenot limited to, DNA-DNA or DNA-RNA hybridizations, PCR amplification,and protein bioassay or immunoassay techniques which include membrane,solution, or chip based technologies for the detection and/orquantification of nucleic acid or protein sequences.

Immunological methods for detecting and measuring the expression of PTAMusing either specific polyclonal or monoclonal antibodies are known inthe art. Examples of such techniques include enzyme-linked immunosorbentassays (ELISAs), radioimmunoassays (RIAs), and fluorescence activatedcell sorting (FACS). A two-site, monoclonal-based immunoassay utilizingmonoclonal antibodies reactive to two non-interfering epitopes on PTAMis preferred, but a competitive binding assay may be employed. These andother assays are well known in the art. (See, e.g., Hampton, R. et al.(1990) Serological Methods, a Laboratory Manual, APS Press, St PaulMinn., Sect. IV; Coligan, J. E. et al. (1997) Current Protocols inImmunology, Greene Pub. Associates and Wiley-Interscience, New YorkN.Y.; and Pound, J. D. (1998) Immunochemical Protocols, Humana Press,Totowa N. J.).

A wide variety of labels and conjugation techniques are known by thoseskilled in the art and may be used in various nucleic acid and aminoacid assays. Means for producing labeled hybridization or PCR probes fordetecting sequences related to polynucleotides encoding PTAM includeoligolabeling, nick translation, end-labeling, or PCR amplificationusing a labeled nucleotide. Alternatively, the sequences encoding PTAM,or any fragments thereof, may be cloned into a vector for the productionof an mRNA probe. Such vectors are known in the art, are commerciallyavailable, and may be used to synthesize RNA probes in vitro by additionof an appropriate RNA polymerase such as T7, T3, or SP6 and labelednucleotides. These procedures may be conducted using a variety ofcommercially available kits, such as those provided by AmershamPharmacia Biotech, Promega (Madison Wis.), and US Biochemical. Suitablereporter molecules or labels which may be used for ease of detectioninclude radionuclides; enzymes, fluorescent, chemiluminescent, orchromogenic agents, as well as substrates, cofactors, inhibitors,magnetic particles, and the like.

Host cells transformed with nucleotide sequences encoding PTAM may becultured under conditions suitable for the expression and recovery ofthe protein from cell culture. The protein produced by a transformedcell may be secreted or retained intracellularly depending on thesequence and/or the vector used. As will be understood by those of skillin the art, expression vectors containing polynucleotides which encodePTAM may be designed to contain signal sequences which direct secretionof PTAM through a prokaryotic or eukaryotic cell membrane.

In addition, a host cell strain may be chosen for its ability tomodulate expression of the inserted sequences or to process theexpressed protein in the desired fashion. Such modifications of thepolypeptide include, but are not limited to, acetylation, carboxylation,glycosylation, phosphorylation, lipidation, and acylation.Post-translational processing which cleaves a “prepro” form of theprotein may also be used to specify protein targeting, folding, and/oractivity. Different host cells which have specific cellular machineryand characteristic mechanisms for post-translational activities (e.g.,CHO, HeLa, MDCK, HEK293, and W138), are available from the American TypeCulture Collection (ATCC, Bethesda Md.) and may be chosen to ensure thecorrect modification and processing of the foreign protein.

In another embodiment of the invention, natural, modified, orrecombinant nucleic acid, sequences encoding PTAM may be ligated to aheterologous sequence resulting in translation of a fusion protein inany of the aforementioned host systems. For example, a chimeric PTAMprotein containing a heterologous moiety that can be recognized by acommercially available antibody may facilitate the screening of peptidelibraries for inhibitors of PTAM activity. Heterologous protein andpeptide moieties may also facilitate purification of fusion proteinsusing commercially available affinity matrices. Such moieties include,but are not limited to, glutathione S-transferase (GST), maltose bindingprotein (MBP), thioredoxin (Trx), calmodulin binding peptide (CBP),6-His, FLAG, c-myc, and hemagglutinin (HA). GST, MBP, Trx, CBP, and6-His enable purification of their cognate fusion proteins onimmobilized glutathione, maltose, phenylarsine oxide, calmodulin, andmetal-chelate resins, respectively. FLAG, c-myc, and hemagglutinin (HA)enable immunoaffinity purification of fusion proteins using commerciallyavailable monoclonal and polyclonal antibodies that specificallyrecognize these epitope tags. A fusion protein may also be-engineered tocontain a proteolytic cleavage site located between the PTAM encodingsequence and the heterologous protein sequence, so that PTAM may becleaved away from the heterologous moiety following purification.Methods for fusion protein expression and purification are discussed inAusubel (1995, supra, ch 10.) A variety of commercially available kitsmay also be used to facilitate expression and purification of fusionproteins.

In a further embodiment of the invention, synthesis of radiolabeled PTAMmay be achieved in vitro using the TNT rabbit reticulocyte lysate orwheat germ extract systems (Promega). These systems couple transcriptionand translation of protein-coding sequences operably associated with theT7, T3, or SP6 promoters. Translation takes place in the presence of aradiolabeled amino acid precursor, preferably ³⁵S-methionine.

Fragments of PTAM may be produced not only by recombinant production,but also by direct peptide synthesis using solid-phase techniques. (See,e.g., Creighton, supra pp. 55-60.) Protein synthesis may be performed bymanual techniques or by automation. Automated synthesis may be achieved,for example, using the ABI 431 A Peptide Synthesizer (Perkin-Elmer).Various fragments of PTAM may be synthesized separately and thencombined to produce the full length molecule.

Therapeutics

Chemical and structural similarity, e.g., in the context of sequencesand motifs, exists between PTAM and protein transport-associatedmolecules. In addition, the expression of PTAM is closely associatedwith cell proliferation. Therefore, in cell proliferative and secretorydisorders where the expression or activity of PTAM is low, it isdesirable to increase the expression or activity of PTAM. In cellproliferative and secretory disorders where the expression or activityof PTAM is high, it is desirable to decrease the expression or activityof PTAM.

Therefore, in one embodiment, PTAM or a fragment or derivative thereofmay be administered to a subject to treat or prevent a disorderassociated with cell proliferation or secretion in which the expressionor activity of PTAM is decreased. Examples of such disorders include,but are not limited to, cancers including adenocarcinoma, leukemia,lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, inparticular, cancers of the adrenal gland, bladder, bone, bone marrow,brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract,heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis,prostate, salivary glands, skin, spleen, testis, thymus, thyroid, anduterus; immune disorders such as actinic keratosis, acquiredimmunodeficiency syndrome (AIDS), Addison's disease, adult respiratorydistress syndrome, allergies, ankylosing spondylitis, amyloidosis,anemia, arteriosclerosis, asthma, atherosclerosis, autoimmune hemolyticanemia, autoimmune thyroiditis, bronchitis, bursitis, cholecystitis,cirrhosis, contact dermatitis, Crohn's disease, atopic dermatitis,dermatomyositis, diabetes mellitus, emphysema, erythroblastosis fetalis,erythema nodosum, atrophic gastritis, glomerulonephritis, Goodpasture'ssyndrome, gout, Graves' disease, Hashimoto's thyroiditis, paroxysmalnocturnal hemoglobinuria, hepatitis, hypereosinophilia, irritable bowelsyndrome, episodic lymphopenia with lymphocytotoxins, mixed connectivetissue disease (MCTD), multiple sclerosis, myasthenia gravis, myocardialor pericardial inflammation, myelofibrosis, osteoarthritis,osteoporosis, pancreatitis, polycythemia vera, polymyositis, psoriasis,Reiter's syndrome, rheumatoid arthritis, scleroderma, Sjögren'ssyndrome, systemic anaphylaxis, systemic lupus erythematosus, systemicsclerosis, primary thrombocythemia, thrombocytopenic purpura, ulcerativecolitis, uveitis, Werner syndrome, complications of cancer,hemodialysis, and extracorporeal circulation, viral, bacterial, fungal,parasitic, protozoal, and helminthic infections, and trauma; andsecretory disorders such as cystic fibrosis, glucose-galactosemalabsorption syndrome, hypercholesterolemia, diabetes insipidus, hyper-and hypoglycemia, goiter, Cushing's disease, and other conditionsassociated with abnormal vesicle trafficking, such as allergies,including hay fever, asthma, and urticaria (hives), autoimmune hemolyticanemia, Chediak-Higashi syndrome, and toxic shock syndrome.

In another embodiment, a vector capable of expressing PTAM or a fragmentor derivative thereof may be administered to a subject to treat orprevent a disorder including, but not limited to, those described above.

In a further embodiment, a pharmaceutical composition comprising asubstantially purified PTAM in conjunction with a suitablepharmaceutical carrier may be administered to a subject to treat orprevent a disorder including, but not limited to, those provided above.

In still another embodiment, an agonist which modulates the activity ofPTAM may be administered to a subject to treat or prevent a disorderincluding, but not limited to, those listed above.

In a further embodiment, an antagonist of PTAM may be administered to asubject to treat or prevent a disorder in which the expression oractivity of PTAM is increased. Examples of such disorders include, butare not limited to, those described above. In one aspect, an antibodywhich specifically binds PTAM may be used directly as an antagonist orindirectly as a targeting or delivery mechanism for bringing apharmaceutical agent to cells or tissue which express PTAM.

In an additional embodiment, a vector expressing the complement of thepolynucleotide encoding PTAM may be administered to a subject to treator prevent a disorder including, but not limited to, those describedabove.

In other embodiments, any of the proteins, antagonists, antibodies,agonists, complementary sequences, or vectors of the invention may beadministered in combination with other appropriate therapeutic agents.Selection of the appropriate agents for use in combination therapy maybe made by one of ordinary skill in the art, according to conventionalpharmaceutical principles. The combination of therapeutic agents may actsynergistically to effect the treatment or prevention of the variousdisorders described above. Using this approach, one may be able toachieve therapeutic efficacy with lower dosages of each agent, thusreducing the potential for adverse side effects.

An antagonist of PTAM may be produced using methods which are generallyknown in the art. In particular, purified PTAM may be used to produceantibodies or to screen libraries of pharmaceutical agents to identifythose which specifically bind PTAM. Antibodies to PTAM may also begenerated using methods that are well known in the art. Such antibodiesmay include, but are not limited to, polyclonal, monoclonal, chimeric,and single chain antibodies, Fab fragments, and fragments produced by aFab expression library. Neutralizing antibodies (i.e., those whichinhibit dimer formation) are especially preferred for therapeutic use.

For the production of antibodies, various hosts including goats,rabbits, rats, mice, humans, and others may be immunized by injectionwith PTAM or with any fragment or oligopeptide thereof which hasimmunogenic properties. Depending on the host species, various adjuvantsmay be used to increase immunological response. Such adjuvants include,but are not limited to, Freund's, mineral gels such as aluminumhydroxide, and surface active substances such as lysolecithin, pluronicpolyols, polyanions, peptides, oil emulsions, KLH, and dinitrophenol.Among adjuvants used in humans, BCG (bacilli Calmette-Guerin) andCorynebacterium parvum are especially preferable.

It is preferred that the oligopeptides, peptides, or fragments used toinduce antibodies to PTAM have an amino acid sequence consisting of atleast about 5 amino acids, and, more preferably, of at least about 10amino acids. It is also preferable that these oligopeptides, peptides,or fragments are identical to a portion of the amino acid sequence ofthe natural protein and contain the entire amino acid sequence of asmall, naturally occurring molecule. Short stretches of PTAM amino acidsmay be fused with those of another protein, such as KLH, and antibodiesto the chimeric molecule may be produced.

Monoclonal antibodies to PTAM may be prepared using any technique whichprovides for the production of antibody molecules by continuous celllines in culture. These include, but are not limited to, the hybridomatechnique, the human B-cell hybridoma technique, and the EBV-hybridomatechnique. (See, e.g., Kohler, G. et al. (1975) Nature 256:495-497;Kozbor, D. et al. (1985) J. Immunol. Methods 81:31-42; Cote, R. J. etal. (1983) Proc. Natl. Acad. Sci. 80:2026-2030; and Cole, S. P. et al.(1984) Mol. Cell Biol. 62:109-120.)

In addition, techniques developed for the production of “chimericantibodies.” such as the splicing of mouse antibody genes to humanantibody genes to obtain a molecule with appropriate antigen specificityand biological activity, can be used. (See, e.g., Morrison, S. L. et al.(1984) Proc. Natl. Acad. Sci. 81 6851-6855; Neuberger, M. S. et al.(1984) Nature 312:604-608; and Takeda, S. et al. (1985) Nature314:452-454.) Alternatively, techniques described for the production ofsingle chain antibodies may be adapted, using methods known in the art,to produce PTAM-specific single chain antibodies. Antibodies withrelated specificity, but of distinct idiotypic composition, may begenerated by chain shuffling from random combinatorial immunoglobulinlibraries. (See, e.g., Burton D. R. (1991) Proc. Natl. Acad. Sci.88:10134-10137.)

Antibodies may also be produced by inducing in vivo production in thelymphocyte population or by screening immunoglobulin libraries or panelsof highly specific binding reagents as disclosed in the literature.(See, e.g., Orlandi, R. et al. (1989) Proc. Natl. Acad. Sci. 86:3833-3837; Winter, G. et al. (1991) Nature 349:293-299.)

Antibody fragments which contain specific binding sites for PTAM mayalso be generated. For example, such fragments include, but are notlimited to, F(ab′)₂ fragments produced by pepsin digestion of theantibody molecule and Fab fragments generated by reducing the disulfidebridges of the F(ab′)₂ fragments. Alternatively, Fab expressionlibraries may be constructed to allow rapid and easy identification ofmonoclonal Fab fragments with the desired specificity. (See, e.g., Huse,W. D. et al. (1989) Science 246:1275-1281.)

Various immunoassays may be used for screening to identify antibodieshaving the desired specificity. Numerous protocols for competitivebinding or immunoradiometric assays using either polyclonal ormonoclonal antibodies with established specificities are well known inthe art. Such immunoassays typically involve the measurement of complexformation between PTAM and its specific antibody. A two-site,monoclonal-based immunoassay utilizing monoclonal antibodies reactive totwo non-interfering PTAM epitopes is preferred, but a competitivebinding assay may also be employed (Pound, supra.)

In another embodiment of the invention, the polynucleotides encodingPTAM, or any fragment or complement thereof, may be used for therapeuticpurposes. In one aspect, the complement of the polynucleotide encodingPTAM may be used in situations in which it would be desirable to blockthe transcription of the mRNA. In particular, cells may be transformedwith sequences complementary to polynucleotides encoding PTAM. Thus,complementary molecules or fragments may be used to modulate PTAMactivity, or to achieve regulation of gene function. Such technology isnow well known in the art, and sense or antisense oligonucleotides orlarger fragments can be designed from various locations along the codingor control regions of sequences encoding PTAM.

Expression vectors derived from retroviruses, adenoviruses, or herpes orvaccinia viruses, or from various bacterial plasmids, may be used fordelivery of nucleotide sequences to the targeted organ, tissue, or cellpopulation. Methods which are well known to those skilled in the art canbe used to construct vectors to express nucleic acid sequencescomplementary to the polynucleotides encoding PTAM. (See; e.g.,Sambrook, supra; Ausubel, 1995, supra.)

Genes encoding PTAM can be turned off by transforming a cell or tissuewith expression vectors which express high levels of a polynucleotide,or fragment thereof, encoding PTAM. Such constructs may be used tointroduce untranslatable sense or antisense sequences into a cell. Evenin the absence of integration into the DNA, such vectors may continue totranscribe RNA molecules until they are disabled by endogenousnucleases. Transient expression may last for a month or more with anon-replicating vector, and may last even longer if appropriatereplication elements are part of the vector system.

As mentioned above, modifications of gene expression can be obtained bydesigning complementary sequences or antisense molecules (DNA, RNA, orPNA) to the control, 5′, or regulatory regions of the gene encodingPTAM. Oligonucleotides derived from the transcription initiation site,e.g., between about positions −10 and +10 from the start site, arepreferred. Similarly, inhibition can be achieved using triple helixbase-pairing methodology. Triple helix pairing is useful because itcauses inhibition of the ability of the double helix to opensufficiently for the binding of polymerases, transcription factors, orregulatory molecules. Recent therapeutic advances using triplex DNA havebeen described in the literature. (See, e.g., Gee, J. E. et al. (1994)in Huber, B. E. and B. I. Carr, Molecular and Immunologic Approaches,Futura Publishing, Mt. Kisco N.Y., pp. 163-177.) A complementarysequence or antisense molecule may also be designed to block translationof mRNA by preventing the transcript from binding to ribosomes.

Ribozymes, enzymatic RNA molecules, may also be used to catalyze thespecific cleavage of RNA. The mechanism of ribozyme action involvessequence-specific hybridization of the ribozyme molecule tocomplementary target RNA, followed by endonucleolytic cleavage. Forexample, engineered hammerhead motif ribozyme molecules may specificallyand efficiently catalyze endonucleolytic cleavage of sequences encodingPTAM.

Specific ribozyme cleavage sites within any potential RNA target areinitially identified by scanning the target molecule for ribozymecleavage sites, including the following-sequences: GUA, GUU, and GUC.Once identified, short RNA sequences of between 15 and 20ribonucleotides, corresponding to the region of the target genecontaining the cleavage site, may be evaluated for secondary structuralfeatures which may render the oligonucleotide inoperable. Thesuitability of candidate targets may also be evaluated by testingaccessibility to hybridization with complementary oligonucleotides usingribonuclease protection assays.

Complementary ribonucleic acid molecules and ribozymes of the inventionmay be prepared by any method known in the art for the synthesis ofnucleic acid molecules. These include techniques for chemicallysynthesizing oligonucleotides such as solid phase phosphoramiditechemical synthesis. Alternatively, RNA molecules may be generated by invitro and in vivo transcription of DNA sequences encoding PTAM. Such DNAsequences may be incorporated into a wide variety of vectors withsuitable RNA polymerase promoters such as T7 or SP6. Alternatively,these cDNA constructs that synthesize complementary RNA, constitutivelyor inducibly, can be introduced into cell lines, cells, or tissues.

RNA molecules may be modified to increase intracellular stability andhalf-life. Possible modifications include, but are riot limited to, theaddition of flanking sequences at the 5′ and/or 3′ ends of the molecule,or the use of phosphorothioate or 2′ O-methyl rather thanphosphodiesterase linkages within the backbone of the molecule. Thisconcept is inherent in the production of PNAs and can be extended in allof these molecules by the inclusion of nontraditional bases such asinosine, queosine, and wybutosine, as well as acetyl-, methyl-, thio-,and similarly modified forms of adenine, cytidine, guanine, thymine, anduridine which are not as easily recognized by endogenous endonucleases.

Many methods for introducing vectors into cells or tissues are availableand equally suitable for use in vivo, in vitro, and ex vivo. For ex vivotherapy, vectors may be introduced into stem cells taken from thepatient and clonally propagated for autologous transplant back into thatsame patient. Delivery by transfection, by liposome injections, or bypolycationic amino polymers may be achieved using methods which are wellknown in the art. (See e.g., Goldman, C. K. et al. (0.1997) NatureBiotechnology 15:462-466.)

Any of the therapeutic methods described above may be applied to anysubject in need of such therapy, including, for example, mammals such asdogs, cats, cows, horses, rabbits, monkeys, and most preferably, humans.

An additional embodiment of the invention relates to the administrationof a pharmaceutical or sterile composition, in conjunction with apharmaceutically acceptable carrier, for any of the therapeutic effectsdiscussed above. Such pharmaceutical compositions may consist of PTAM,antibodies to PTAM, and mimetics, agonists, antagonists, or inhibitorsof PTAM. The compositions may be administered alone or in combinationwith at least one other agent, such as a stabilizing compound, which maybe administered in any sterile, biocompatible pharmaceutical carrierincluding, but not limited to, saline, buffered saline, dextrose, andwater. The compositions may be administered to a patient alone, or incombination with other agents, drugs, or hormones.

The pharmaceutical compositions utilized in this invention may beadministered by any number of routes including, but not limited to,oral, intravenous, intramuscular, intra-arterial, intramedullary,intrathecal, intraventricular, transdermal, subcutaneous,intraperitoneal, intranasal, enteral, topical, sublingual, or rectalmeans.

In addition to the active ingredients, these pharmaceutical compositionsmay contain suitable pharmaceuticallv-acceptable carriers comprisingexcipients and auxiliaries which facilitate processing of the activecompounds into preparations which can be used pharmaceutically. Furtherdetails on techniques for formulation and administration may be found inthe latest edition of Remington's Pharmaceutical Sciences (MaackPublishing, Easton Pa.).

Pharmaceutical compositions for oral administration can be formulatedusing pharmaceutically acceptable carriers well known in the art indosages suitable for oral administration. Such carriers enable thepharmaceutical compositions to be formulated as tablets, pills, dragees,capsules, liquids, gels, syrups, slurries, suspensions, and the like,for ingestion by the patient.

Pharmaceutical preparations for oral use can be obtained throughcombining active compounds with solid excipient and processing theresultant mixture of granules (optionally, after grinding) to obtaintablets or dragee cores. Suitable auxiliaries can be added, if desired.Suitable excipients include carbohydrate or protein fillers, such assugars, including lactose, sucrose, mannitol, and sorbitol; starch fromcorn, wheat, rice, potato, or other plants; cellulose, such as methylcellulose, hydroxypropylmethyl-cellulose, or sodiumcarboxymethylcellulose; gums, including arabic and tragacanth; andproteins, such as gelatin and collagen. If desired, disintegrating orsolubilizing agents may be added, such as the cross-linked polyvinylpyrrolidone, agar, and alginic acid or a salt thereof, such as sodiumalginate.

Dragee cores may be used in conjunction with suitable coatings, such asconcentrated sugar solutions, which may also contain gum arabic, talc,polyvinylpyrrolidone, carbopol gel, polyethylene glycol, and/or titaniumdioxide, lacquer solutions, and suitable organic solvents or solventmixtures. Dyestuffs or pigments may be added to the tablets or drageecoatings for product identification or to characterize the quantity ofactive compound, i.e., dosage.

Pharmaceutical preparations which can be used orally include push-fitcapsules made of gelatin, as well as soft, sealed capsules made ofgelatin and a coating, such as glycerol or sorbitol; Push-fit capsulescan contain active ingredients mixed with fillers or binders, such aslactose or starches, lubricants, such as talc or magnesium stearate,and, optionally, stabilizers. In soft capsules, the active compounds maybe dissolved or suspended in suitable liquids, such as fatty oils,liquid, or liquid polyethylene glycol with or without stabilizers.

Pharmaceutical formulations suitable for parenteral administration maybe formulated in aqueous solutions, preferably in physiologicallycompatible buffers such as Hanks' solution, Ringer's solution, orphysiologically buffered saline. Aqueous injection suspensions maycontain substances which increase the viscosity of the suspension, suchas sodium carboxymethyl cellulose, sorbitol, or dextran. Additionally,suspensions of the active compounds maybe prepared as appropriate oilyinjection suspensions. Suitable lipophilic solvents or vehicles includefatty oils, such as sesame oil, or synthetic fatty acid esters, such asethyl oleate, triglycerides, or liposomes. Non-lipid polycationic aminopolymers may also be used for delivery. Optionally, the suspension mayalso contain suitable stabilizers or agents to increase the solubilityof the compounds and allow for the preparation of highly concentratedsolutions.

For topical or nasal administration, penetrants appropriate to theparticular barrier to be permeated are used in the formulation. Suchpenetrants are generally known in the art.

The pharmaceutical compositions of the present invention may bemanufactured in a manner that is known in the art, e.g., by means ofconventional mixing, dissolving, granulating, dragee-making, levigating,emulsifying, encapsulating, entrapping, or lyophilizing processes.

The pharmaceutical composition may be provided as a salt and can beformed with many acids, including but not limited to, hydrochloric,sulfuric, acetic, lactic, tartaric, malic, and succinic acid. Salts tendto be more soluble in aqueous or other protonic solvents than are thecorresponding free base forms. In other cases, the preferred preparationmay be a lyophilized powder which may contain any or all of thefollowing: 1 mM to 50 mM histidine, 0.1% to 2% sucrose, and 2% to 7%mannitol, at a pH range of 4.5 to 5.5, that is combined with bufferprior to use.

After pharmaceutical compositions have been prepared, they can be placedin an appropriate container and labeled for treatment of an indicatedcondition. For administration of PTAM, such labeling would includeamount, frequency, and method of administration.

Pharmaceutical compositions suitable for use in the invention includecompositions wherein the active ingredients are contained in aneffective amount to achieve the intended purpose. The determination ofan effective dose is well within the capability of those skilled in theart.

For any compound, the therapeutically effective dose can be estimatedinitially either in cell culture assays, e.g., of neoplastic cells or inanimal models such as mice, rats, rabbits, dogs, or pigs. An animalmodel may also be used to determine the appropriate concentration rangeand route of administration. Such information can then be used todetermine useful doses and routes for administration in humans.

A therapeutically effective dose refers to that amount of activeingredient, for example PTAM or fragments thereof, antibodies of PTAM,and agonists, antagonists or inhibitors of PTAM, which ameliorates thesymptoms or condition. Therapeutic efficacy and toxicity may bedetermined by standard pharmaceutical procedures in cell cultures orwith experimental animals, such as by calculating the ED₅₀ (the dosetherapeutically effective in 50% of the population) or LD₅₀ (the doselethal to 50% of the population) statistics. The dose ratio oftherapeutic to toxic effects is the therapeutic index, and it can beexpressed as the ED₅₀/LD₅₀. Ratio. Pharmaceutical compositions whichexhibit large therapeutic indices are preferred. The data obtained fromcell culture assays and animal studies are used to formulate a range ofdosage for human use. The dosage contained in such compositions ispreferably within a range of circulating concentrations that includesthe ED₅₀ with little or no toxicity. The dosage varies within this rangedepending upon the dosage form employed, the sensitivity of the patient,and the route of administration.

The exact dosage will be determined by the practitioner, in light offactors related to the subject requiring treatment. Dosage andadministration are adjusted to provide sufficient levels of the activemoiety or to maintain the desired effect. Factors which may be takeninto account include the severity of the disease state, the generalhealth of the subject, the age, weight, and gender of the subject, timeand frequency of administration, drug combination(s), reactionsensitivities, and response to therapy. Long-acting pharmaceuticalcompositions may be administered every 3 to 4 days, every week, orbiweekly depending on the half-life and clearance rate of the particularformulation.

Normal dosage amounts may vary from about 0.1 μg to 100,000 μg, up to atotal dose of about 1 gram, depending upon the route of administration.Guidance as to particular dosages and methods of delivery is provided inthe literature and generally available to practitioners in the art.Those skilled in the art will employ different formulations fornucleotides than for proteins or their inhibitors. Similarly, deliveryof polynucleotides or polypeptides will be specific to particular cells,conditions, locations, etc.

Diagnostics

In another embodiment, antibodies which specifically bind PTAM may beused for the diagnosis of cell proliferative and secretory disorderscharacterized by expression of PTAM; or in assays to monitor patientsbeing treated with PTAM or agonists, antagonists, or inhibitors of PTAM.Antibodies useful for diagnostic purposes may be prepared in the samemanner as described above for therapeutics, Diagnostic assays for PTAMinclude methods which utilize the antibody and a label to detect PTAM inhuman body fluids or in extracts of cells or tissues. The antibodies maybe used with or without modification, and may be labeled by covalent ornon-covalent attachment of a reporter molecule. A wide variety ofreporter molecules, several of which are described above, are known inthe art and may be used.

A variety of protocols for measuring PTAM, including ELISAs, RIAs, andFACS, are known in the art and provide a basis for diagnosing altered orabnormal levels of PTAM expression. Normal or standard values for PTAMexpression are established by combining body fluids or cell extractstaken from normal mammalian subjects, preferably human, with antibody toPTAM under conditions suitable for complex formation. The amount ofstandard complex formation may be quantitated by various methods,preferably by photometric means. Quantities of PTAM expressed insubject, control, and disease samples from biopsied tissues are comparedwith the standard values. Deviation between standard and subject valuesestablishes the parameters for diagnosing disease.

In another embodiment of the invention, the polynucleotides encodingPTAM may be used for diagnostic purposes. The polynucleotides which maybe used include oligonucleotide sequences, complementary RNA and DNAmolecules, and PNAs. The polynucleotides may be used to detect andquantitate gene expression in biopsied tissues in which expression ofPTAM may be correlated with disease. The diagnostic assay may be used todetermine absence, presence, and excess expression of PTAM, and tomonitor regulation of PTAM levels during therapeutic intervention.

In one aspect, hybridization with PCR probes which are capable ofdetecting polynucleotide sequences, including genomic sequences,encoding PTAM or closely related molecules may be used to identifynucleic acid sequences which encode PTAM. The specificity of the probe,whether it is made from a highly specific region, e.g., the 5′regulatory region, or from a less specific region, e.g., a conservedmotif, and the stringency of the hybridization or amplification(maximal, high, intermediate, or low), will determine whether the probeidentifies only naturally occurring sequences encoding PTAM, allelicvariants, or related sequences.

Probes may also be used for the detection of related sequences, andshould preferably have at least 50% sequence identity to any of the PTAMencoding sequences. The hybridization probes of the subject inventionmay be DNA or RNA and may be derived from the sequence of SEQ ID NO:9-16or from genomic sequences including promoters, enhancers, and introns ofthe PTAM gene.

Means for producing specific hybridization probes for DNAs encoding PTAMinclude the cloning of polynucleotide sequences encoding PTAM or PTAMderivatives into vectors for the production of mRNA probes. Such vectorsare known in the art, are commercially available, and may be used tosynthesize RNA probes in vitro by means of the addition of theappropriate RNA polymerases and the appropriate labeled nucleotides.Hybridization probes may be labeled by a variety of reporter groups, forexample, by radionuclides such as ³²P or ³²S, or by enzymatic labels,such as alkaline phosphatase coupled to the probe via avidin/biotincoupling systems, and the like.

Polynucleotide sequences encoding PTAM may be used for the diagnosis ofcell proliferative and secretory disorders associated with expression ofPTAM. Examples of such disorders include, but are not limited to, cellproliferative disorders such as cancers, including adenocarcinoma,leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, inparticular, cancers of the adrenal gland, bladder, bone, bone marrow,brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract,heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis,prostate, salivary glands, skin, spleen, testis, thymus, thyroid, anduterus; immune disorders such as actinic keratosis, acquiredimmunodeficiency syndrome (AIDS), Addison's disease, adult respiratorydistress syndrome, allergies, ankylosing spondylitis, amyloidosis,anemia, arteriosclerosis, asthma, atherosclerosis, autoimmune hemolyticanemia, autoimmune thyroiditis, bronchitis, bursitis, cholecystitis,cirrhosis, contact dermatitis, Crohn's disease, atopic dermatitis,dermatomyositis, diabetes mellitus, emphysema, erythroblastosis fetalis,erythema nodosum, atrophic gastritis, glomerulonephritis, Goodpasture'ssyndrome, gout, Graves' disease, Hashimoto's thyroiditis, paroxysmalnocturnal hemoglobinuria, hepatitis, hypereosinophilia, irritable bowelsyndrome, episodic lymphopenia with lymphocylotoxins, mixed connectivetissue disease (MCTD), multiple sclerosis, myasthenia gravis, myocardialor pericardial inflammation, myelofibrosis, osteoarthritis,osteoporosis, pancreatitis, polycythemia vera, polymyositis, psoriasis,Reiter's syndrome, rheumatoid arthritis, scleroderma, Sjögren'ssyndrome, systemic anaphylaxis, systemic lupus erythematosus, systemicsclerosis, primary thrombocythemia, thrombocytopenic purpura, ulcerativecolitis, uveitis, Werner syndrome, complications of cancer,hemodialysis, and extracorporeal circulation, viral, bacterial, fungal,parasitic, protozoal, and helminthic infections, and trauma; andsecretory disorders such as cystic fibrosis, glucose-galactosemalabsorption syndrome, hypercholesterolemia, diabetes insipidus, hyper-and hypoglycemia, goiter, Cushing's disease, and other conditionsassociated with abnormal vesicle trafficking, such as allergies,including hay fever, asthma, and urticaria (hives), autoimmune hemolyticanemia, Chediak-Higashi syndrome, and toxic shock syndrome. Thepolynucleotide sequences encoding PTAM may be used in Southern ornorthern analysis, dot blot, or other membrane-based technologies; inPCR technologies: in dipstick, pin, and ELISA assays; and in microarraysutilizing fluids or tissues from patients to detect altered PTAMexpression. Such qualitative or quantitative methods are well known inthe art.

In a particular aspect, the nucleotide sequences encoding PTAM may beuseful in assays that detect the presence of associated disorders,particularly those mentioned above. The nucleotide sequences encodingPTAM may be labeled by standard methods and added to a fluid or tissuesample from a patient under conditions suitable for the formation ofhybridization complexes. After a suitable incubation period, the sampleis washed and the signal is quantitated and compared with a standardvalue. If the amount of signal in the patient sample is significantlyaltered in comparison to a control sample then the presence of alteredlevels of nucleotide sequences encoding PTAM in the sample indicates thepresence of the associated disorder: Such assays may also be used toevaluate the efficacy of a particular therapeutic treatment regimen inanimal studies, in clinical trials, or to monitor the treatment of anindividual patient.

In order to provide a basis for the diagnosis of a disorder associatedwith expression of PTAM, a normal or standard profile for expression isestablished. This may be accomplished by combining body fluids or cellextracts taken from normal subjects, either animal or human, with asequence, or a fragment thereof, encoding PTAM, under conditionssuitable for hybridization or amplification. Standard hybridization maybe quantified by comparing the values obtained from normal subjects withvalues from an experiment in which a known amount of a substantiallypurified polynucleotide is used. Standard values obtained in this mannermay be compared with values obtained from samples from patients who aresymptomatic for a disorder. Deviation from standard values is used toestablish the presence of a disorder.

Once the presence of a disorder is established and a treatment protocolis initiated, hybridization assays may be repeated on a regular basis todetermine if the level of expression in the patient begins toapproximate that which is observed in the normal subject. The resultsobtained from successive assays may be used to show the efficacy oftreatment over a period ranging from several days to months.

With respect to cancer, the presence of an abnormal amount of transcript(either under- or over-expressed) in biopsied tissue from an individualmay indicate a predisposition for the development of the disease, or mayprovide a means for detecting the disease prior to the appearance ofactual clinical symptoms. A more definitive diagnosis of this type mayallow health professionals to employ preventative measures or aggressivetreatment earlier thereby preventing the development or furtherprogression of the cancer.

Additional diagnostic uses for oligonucleotides designed from thesequences encoding PTAM may involve the use of PCR. These oligomers maybe chemically synthesized, generated enzymatically, or produced invitro. Oligomers will preferably contain a fragment of a polynucleotideencoding PTAM, or a fragment of a polynucleotide complementary to thepolynucleotide encoding PTAM, and will be employed under optimizedconditions for identification of a specific gene or condition. Oligomersmay also be employed under less stringent conditions for detection orquantitation of closely related DNA or RNA sequences.

Methods which may also be used to quantitate the expression of PTAMinclude radiolabeling or biotinylating nucleotides, coamplification of acontrol nucleic acid, and interpolating results from standard curves.(See, e.g., Melby, P. C. et al. (1993) J. Immunol. Methods 159:235-244;Duplaa, C. et al. (1993) Anal. Biochem. 229-236.) The speed ofquantitation of multiple samples may be accelerated by running the assayin an ELISA format where the oligomer of interest is presented invarious dilutions and a spectrophotometric or colorimetric responsegives rapid quantitation.

In further embodiments, oligonucleotides or longer fragments derivedfrom any of the polynucleotide sequences described herein may be used astargets in a microarray. The microarray can be used to monitor theexpression level of large numbers of genes simultaneously and toidentify genetic variants, mutations, and polymorphisms. Thisinformation may be used to determine gene function, to understand thegenetic basis of a disorder, to diagnose a disorder, and to develop andmonitor the activities of therapeutic agents.

Microarrays may be prepared, used, and analyzed using methods known inthe art. (See, e.g., Brennan, T. M. et al. (1995) U.S. Pat. No.5,474,796; Schena, M. et al. (1996) Proc. Natl. Acad. Sci.93:10614-10619; Baldeschweiler et al. (1995) PCT applicationWO95/251116; Shalon, D. et al. (1995) PCT application WO95/35505;Heller, R. A. et al. (1997) Proc. Natl. Acad. Sci. 94:2150-2155; andHeller, M. J. et al. (1997) U.S. Pat. No. 5,605,662.)

In another embodiment of the invention, nucleic acid sequences encodingPTAM may be used to generate hybridization probes useful in mapping thenaturally occurring genomic sequence. The sequences may be mapped to aparticular chromosome, to a specific region of a chromosome, or toartificial chromosome constructions, e.g., human artificial chromosomes(HACs), yeast artificial chromosomes (YACs), bacterial artificialchromosomes (BACs), bacterial P1 constructions, or single chromosomecDNA libraries. (See, e.g., Harrington, J. J. et al. (1997) Nat Genet.15:345-355; Price, C. M. (1993) Blood Rev. 7:127-134; and Trask, B. J.(1991) Trends Genet. 7:149-154.)

Fluorescent in situ hybridization (FISH) may be correlated with otherphysical chromosome mapping techniques and genetic map data. (See, e.g.,Heinz-Ulrich, et at. (1995) in Meyers, supra, pp. 965-968.) Examples ofgenetic map data can be found in various scientific journals or at theOnline Mendelian Inheritance in Man (OMIM) site. Correlation between thelocation of the gene encoding PTAM on a physical chromosomal map and aspecific disorder, or a predisposition to a specific disorder, may helpdefine the region of DNA associated with that disorder. The nucleotidesequences of the invention may be used to detect differences in genesequences among normal, carrier, and affected individuals.

In situ hybridization of chromosomal preparations and physical mappingtechniques, such as linkage analysis using established chromosomalmarkers, may be used for extending genetic maps. Often the placement ofa gene on the chromosome of another mammalian species, such as mouse,may reveal associated markers even if the number or arm of a particularhuman chromosome is not known. New sequences can be assigned tochromosomal arms by physical mapping. This provides valuable informationto investigators searching for disease genes using positional cloning orother gene discovery techniques. Once the disease or syndrome has beencrudely localized by genetic linkage to a particular genomic region,e.g., ataxia-telangiectasia to 11q22-23, any sequences mapping to thatarea may represent associated or regulatory genes for furtherinvestigation. (See, e.g., Gatti, R. A. et al. (1988) Nature336:577-580.). The nucleotide sequence of the subject invention may alsobe used to detect differences in the chromosomal location due totranslocation, inversion, etc., among normal, carrier, or affectedindividuals.

In another embodiment of the invention, PTAM, its catalytic orimmunogenic fragments, or oligopeptides thereof can be used forscreening libraries of compounds in any of a variety of drug screeningtechniques. The fragment employed in such screening may be free insolution, affixed to a solid support, borne on a cell surface, orlocated intracellularly. The formation of binding complexes between PTAMand the agent being tested may be measured.

Another technique for drug screening provides for high throughputscreening of compounds having suitable binding affinity to the proteinof interest. (See, e.g., Geysen, et al. (1984) PCT applicationWO84103564.) In this method, large numbers of different small testcompounds are synthesized on a solid substrate. The test compounds arereacted with PTAM, or fragments thereof, and washed. Bound PTAM is thendetected by methods well known in the art. Purified PTAM can also becoated directly onto plates for use in the aforementioned drug screeningtechniques. Alternatively, non-neutralizing antibodies can be used tocapture the peptide and immobilize it on a solid support.

In another embodiment, one may use competitive drug screening assays inwhich neutralizing antibodies capable of binding PTAM specificallycompete with a test compound for binding PTAM. In this manner,antibodies can be used to detect the presence of any peptide whichshares one or more antigenic determinants with PTAM.

In additional embodiments, the nucleotide sequences which encode PTAMmay be used in any molecular biology techniques that have yet id bedeveloped, provided the new techniques rely on properties of nucleotidesequences that are currently known, including, but not limited to, suchproperties as the triplet genetic code and specific base pairinteractions.

Without further elaboration, it is believed that one skilled in the artcan, using the preceding description, utilize the present invention toits fullest extent. The following preferred specific embodiments are,therefore, to be construed as merely illustrative, and not limitative ofthe remainder of the disclosure in any way whatsoever.

The disclosures of all patents, applications, and publications mentionedabove and below, in particular U.S. Ser. No. 60/098,206, are herebyexpressly incorporated by reference.

EXAMPLES

I. Construction of cDNA Libraries

RNA was purchased from Clontech or isolated from tissues described inTable 4. Some tissues were homogenized and lysed in guanidiniumisothiocyanate, while others were homogenized and lysed in phenol or ina suitable mixture of denaturants, such as TRIZOL (Life Technologies), amonophasic solution of phenol and guanidine isothiocyanate. Theresulting lysates were centrifuged over CsCl cushions or extracted withchloroform. RNA was precipitated from the lysates with eitherisopropanol or sodium acetate and ethanol, or by other routine methods.

Phenol extraction and precipitation of RNA were repeated as necessary toincrease RNA purity. In some cases, RNA was treated with DNase. For mostlibraries, poly(A+) RNA was isolated using oligo d(T)-coupledparamagnetic particles (Promega), OLIGOTEX latex particles (QIAGEN,Valencia Calif.), or an OLIGOTEX mRNA purification kit (QIAGEN).Alternatively, RNA was isolated directly from tissue lysates using otherRNA isolation kits, e.g., the POLY(A)PURE mRNA purification kit (Ambion,Austin Tex.).

In some cases, Stratagene was provided with RNA and constructed thecorresponding cDNA libraries. Otherwise, cDNA was synthesized and cDNAlibraries were constructed with the UNIZAP vector system (Stratagene) orSUPERSCRIPT plasmid system (Life Technologies), using the recommendedprocedures or similar methods known in the art. (See, e.g., Ausubel,1997, supra, units 5.1-6.6.) Reverse transcription was initiated usingoligo d(T) or random primers. Synthetic oligonucleotide adapters wereligated to double stranded cDNA, and the cDNA was digested with theappropriate restriction enzyme or enzymes. For most libraries, the cDNAwas size-selected (300-1000 bp) using SEPHACRYL S1000, SEPHAROSE CL2B,or SEPHAROSE CL4B column chromatography (Amersham Pharmacia Biotech) orpreparative agarose gel electrophoresis. cDNAs were ligated intocompatible restriction enzyme sites of the polylinker of a suitableplasmid, e.g., PBLUESCRIPT plasmid (Stratagene), PSPORT1 plasmid (LifeTechnologies), or pINCY (Incyte Pharmaceuticals, Palo Alto Calif.).Recombinant plasmids were transformed into competent E. coli cellsincluding XL1-Blue, XL1-BlueMRF, or SOLR from Stratagene or DH5α, DH10B, or ElectroMAX DH10B from Life Technologies. II.

Isolation of cDNA Clones

Plasmids were recovered from host cells by in vivo excision, using theUNIZAP vector system (Stratagene) or cell lysis. Plasmids were purifiedusing at least one of the following: a MAGIC or WIZARD Minipreps DNApurification system (Promega); an AGTC Miniprep purification kit (EdgeBiosystems, Gaithersburg Md.); and QIAWELL 8 Plasmid, QIAWELL 8 PlusPlasmid, QIAWELL 8 Ultra Plasmid purification systems or the REAL Prep96 plasmid kit from QIAGEN. Following precipitation, plasmids wereresuspended in 0.11 ml of distilled water and stored, with or withoutlyophilization, at 4° C.

Alternatively, plasmid DNA was amplified from host cell lysates usingdirect link PCR in a high-throughput format (Rao, V. B. (11994) Anal.Biochem. 216:1-14.) Host cell lysis and thermal cycling steps werecarried out in a single reaction mixture. Samples were processed andstored in 384-well plates, and the concentration of amplified plasmidDNA was quantified fluorometrically using PICOGREEN dye (MolecularProbes, Eugene Oreg.) and a Fluoroskan II fluorescence scanner(Labsystems Oy, Helsinki, Finland).

III. Sequencing and Analysis

The cDNAs were prepared for sequencing using the ABI CATALYST 800(Perkin-Elmer) or the HYDRA microdispenser (Robbins Scientific,Sunnyvale Calif.) or MICROLAB 2200 (Hamilton, Reno Nev.) systems incombination with the PTC-200 thermal cyclers (MJ Research, WatertownMass.). The cDNAs were sequenced using the ABI PRISM 373 or 377sequencing systems (Perkin-Elmer) and standard ABI protocols, basecalling software, and kits. In one alternative, cDNAs were sequencedusing the MEGABACE 1000 capillary electrophoresis sequencing system(Molecular Dynamics, Sunnyvale Calif.). In another alternative, thecDNAs were amplified and sequenced using the ABI PRISM BIGDYE Terminatorcycle sequencing ready reaction kit (Perkin-Elmer). In yet anotheralternative, cDNAs were sequenced using solutions dyes from AmershamPharmacia Biotech. Reading frames for the ESTs were determined usingstandard methods (reviewed in Ausubel, 1997, supra, unit 7.7.) Some ofthe cDNA sequences were selected for extension using the techniquesdisclosed in Example V.

The polynucleotide sequences derived from cDNA, extension, and shotgunsequencing were assembled and analyzed using a combination of softwareprograms which utilize algorithms well known to those skilled in theart. Table 5 summarizes the software programs, descriptions, references,and threshold parameters used. The first column of Table 5 shows thetools, programs, and algorithms used, the second column provides a briefdescription thereof, the third column presents the references which areincorporated by reference herein, and the fourth column presents, whereapplicable, the scores, probability values, and other parameters used toevaluate the strength of a match between two sequences (the higher theprobability the greater the homology). Sequences were analyzed usingMACDNASIS PRO software (Hitachi Software Engineering, S. San FranciscoCalif.) and LASERGENE software (DNASTAR).

The polynucleotide sequences were validated by removing vector, linker,and polyA sequences and by masking ambiguous bases, using algorithms andprograms based on BLAST, dynamic programing, and dinucleotide nearestneighbor analysis. The sequences were then queried against a selectionof public databases such as GenBank primate, rodent, mammalian,vertebrate, and eukaryote databases, and BLOCKS to acquire annotation,using programs based on BLAST, FASTA, and BLIMPS. The sequences wereassembled into full length polynucleotide sequences using programs basedon Phred, Phrap, and Consed, and were screened for open reading framesusing programs based on GeneMark, BLAST, and FASTA. The full lengthpolynucleotide sequences were translated to derive the correspondingfull length amino acid sequences, and these full length sequences weresubsequently analyzed by querying against databases such as the GenBankdatabases (described above), SwissProt, BLOCKS, PRINTS, PFAM, andProsite.

The programs described above for the assembly and analysis of fulllength polynucleotide and amino acid sequences were also used toidentify polynucleotide sequence fragments from SEQ ID NO:8-14.Fragments from about 20 to about 4000 nucleotides which are useful inhybridization and amplification technologies were described in TheInvention section above.

IV. Northern Analysis

Northern analysis is a laboratory technique used to detect the presenceof a transcript of a gene and involves the hybridization of a labelednucleotide sequence to a membrane on which RNAs from a particular celltype or tissue have been bound. (See, e.g., Sambrook, supra, ch. 7;Ausubel, 1995, supra, ch. 4 and 16.)

Analogous computer techniques applying BLAST were used to search foridentical or related molecules in nucleotide databases such as GenBankor LIFESEQ database (Incyte Pharmaceuticals). This analysis is muchfaster than multiple membrane-based hybridizations. In addition, thesensitivity of the computer search can be modified to determine whetherany particular match is categorized as exact or similar. The basis ofthe search is the product score, which is defined as:$\frac{\%\quad{sequence}\quad{identity}\quad \times \%\quad{maximum}\quad{BLAST}\quad{score}}{100}$The product score takes into account both the degree of similaritybetween two sequences and the length of the sequence match. For example,with a product score of 40, the match will be exact within a 1% to 2%error, and, with a product score of 70, the match will be exact. Similarmolecules are usually identified by selecting those which show productscores between 15 and 40, although lower scores may identify relatedmolecules.

The results of northern analyses are reported as a list of libraries inwhich the transcript encoding PTAM occurred. Abundance and percentabundance are also reported. Abundance directly reflects the number oftimes a particular transcript is represented in a cDNA library, andpercent abundance is abundance divided by the total number of sequencesexamined in the cDNA library. Further analyses produced the percentagevalues of tissue-specific and disease expression which are reported inTable 3.

V. Extension of PTAM Encoding Polynucleotides

The nucleic acid sequences of Incyte ESTs 12033, 1209687, 1717058,1749964, 1856357, 1871275, 2645806, and 3437773 were used to designoligonucleotide primers for extending partial nucleotide sequence tofull length. For each nucleic acid sequence, one primer was synthesizedto initiate extension of an antisense polynucleotide, and the other wassynthesized to initiate extension of a sense polynucleotide. Primerswere used to facilitate the extension of the known sequence “outward”which generates amplicons containing new unknown nucleotide sequence forthe region of interest. The initial primers were designed from the cDNAusing OLIGO 4.06 software (National Biosciences), or another appropriateprogram, to be about 22 to 30 nucleotides in length, to have a GCcontent of about 50% or more, and to anneal to the target sequence attemperatures of about 68° C. to about 72° C. Any stretch of nucleotideswhich would result in hairpin structures and primer-primer dimerizationswas avoided.

Selected human cDNA libraries (Life Technologies) were used to extendthe sequence. If more than one extension is necessary or desired,additional sets of primers are designed to further extend the knownregion.

High fidelity amplification was obtained by following the instructionsfor the XL-PCR kit (Perkin-Elmer) and thoroughly mixing the enzyme andreaction mix. PCR was performed using the PTC200 thermal cycler (M. J.Research) beginning with 40 pmol of each primer and the recommendedconcentrations of all other components of the kit, with the followingparameters:

Step 1 94° C. for 1 min (initial denaturation) Step 2 65° C. for 1 minStep 3 68° C. for 6 min Step 4 94° C. for 15 sec Step 5 65° C. for 1 minStep 6 68° C. for 7 min Step 7 Repeat steps 4-6 for an additional 15cycles Step 8 94° C. for 15 sec Step 9 65° C. for 1 min Step 10 68° C.for 7:15 min Step 11 Repeat steps 8-10 for an additional 12 cycles Step12 72° C. for 8 min Step 13 4° C. (and holding)

A 5 μl to 10 μl aliquot of the reaction mixture was analyzed byelectrophoresis on a low concentration (about 0.6% to 0.8%) agarosemini-gel to determine which reactions were successful in extending thesequence. Bands thought to contain the largest products were excisedfrom the gel, purified using the QIAQUICK kit (QIAGEN), and trimmed ofoverhangs using Klenow enzyme to facilitate religation and cloning.

After ethanol precipitation, the products were redissolved in 13 μl ofligation buffer, 1 μl T4-DNA ligase (15 units) and 1 μl T4polynucleotide kinase were added, and the mixture was incubated at roomtemperature for 2 to 3 hours, or overnight at 16° C. Competent E. colicells (in 40 μu of appropriate media) were transformed with 3 μl ofligation mixture and cultured in 80 μl of SOC medium. (See, e.g.,Sambrook, supra, Appendix A, p. 2.) After incubation for one hour at 37°C., the E. coli mixture was plated on Luria Bertani (LB) agar (See,e.g., Sambrook, supra, Appendix A, p. 1) containing carbenicillin(2×carb). The following day, several colonies were randomly picked fromeach plate and cultured in 150 μl of liquid LB/2×carb medium placed inan individual well of an appropriate commercially-available sterile96-well microtiter plate. The following day, 5 μl of each overnightculture was transferred into a non-sterile 96-well plate and, afterdilution 1:10 with water, 5 μl from each sample was transferred into aPCR array.

For PCR amplification, 18 μl of concentrated PCR reaction mix (3.3×)containing 4 units of rTth DNA polymerase, a vector primer, and one orboth of the gene specific primers used for the extension reaction wereadded to each well. Amplification was performed using the followingconditions:

Step 1 94° C. for 60 sec Step 2 94° C. for 20 sec Step 3 55° C. for 30sec Step 4 72° C. for 90 sec Step 5 Repeat steps 2-4 for an additional29 cycles Step 6 72° C. for 180 sec Step 7 4° C. (and holding)

Aliquots of the PCR reactions were run on agarose gels together withmolecular weight markers. The sizes of the PCR products were compared tothe original partial cDNAs, and appropriate clones were selected,ligated into plasmid, and sequenced.

In like manner, the nucleotide sequences of SEQ ID NO:9-16 are used toobtain 5′ regulatory sequences using the procedure above,oligonucleotides designed for 5′ extension, and an appropriate genomiclibrary.

VI. Labeling and Use of Individual Hybridization Probes

Hybridization probes derived from SEQ ID NO:9-16 are employed to screencDNAs, genomic DNAs, or mRNAs. Although the labeling ofoligonucleotides, consisting of about 20 base pairs, is specificallydescribed, essentially the same procedure is used with larger nucleotidefragments. Oligonucleotides are designed using state-of-the-art softwaresuch as OLIGO 4.06 software (National Biosciences) and labeled bycombining 50 pmol of each oligomer, 250 μci of [γ−³²P] adenosinetriphosphate (Amersham Pharmacia Biotech), and T4 polynucleotide kinase(DuPont NEN, Boston Mass.). The labeled oligonucleotides aresubstantially purified using a SEPHADEX G-25 superfine size exclusiondextran bead column (Amersham Pharmacia Biotech). An aliquot containing10⁷ counts per minute of the labeled probe is used in a typicalmembrane-based hybridization analysis of human genomic DNA digested withone of the following endonucleases: Ase I, Bgl II, Eco RI, Pst I, XbaI,or Pvu II (DuPont NEN).

The DNA from each digest is fractionated on a 0.7% agarose gel andtransferred to NYTRAN PLUS, nylon membranes (Schleicher & Schuell,Durham N.H.). Hybridization is carried out for 16 hours at 40° C. Toremove nonspecific signals, blots are sequentially washed at roomtemperature under increasingly stringent conditions up to 0.1×salinesodium citrate and 0.5% sodium dodecyl sulfate. After XOMAT-AR film(Eastman Kodak, Rochester N.Y.) is exposed to the blots to film forseveral hours, hybridization patterns are compared visually.

VII. Microarrays

A chemical coupling procedure and an ink jet device can be used tosynthesize array elements on the surface of a substrate. (See, e.g.,Baldeschweiler, supra.) An array analogous to a dot or slot blot mayalso be used to arrange and link elements to the surface of a substrateusing thermal, UV, chemical, or mechanical bonding procedures. A typicalarray may be produced by hand or using available methods and machinesand contain any appropriate number of elements. After hybridization,nonhybridized probes are removed and a scanner used to determine thelevels and patterns of fluorescence. The degree of complementarity andthe relative abundance of each probe which hybridizes to an element onthe microarray may be assessed through analysis of the scanned images.

Full-length cDNAs, Expressed Sequence Tags (ESTs), or fragments thereofmay comprise the elements of the microarray. Fragments suitable forhybridization can be selected using software well known in the art suchas LASERGENE software (DNASTAR). Full-length cDNAs, ESTs, or fragmentsthereof corresponding to one of the nucleotide sequences of the presentinvention, or selected at random from a cDNA library relevant to thepresent invention, are arranged on an appropriate substrate, e.g., aglass slide. The cDNA is fixed to the slide using, e.g., UVcross-linking followed by thermal and chemical treatments and subsequentdrying. (See, e.g., Schena, M. et al. (1995) Science 270:467-470;Shalon, D. et al. (1996) Genome Res. 6:639-645.) Fluorescent probes areprepared and used for hybridization to the elements on the substrate.The substrate is analyzed by procedures described above.

VIII. Complementary Polynucleotides

Sequences complementary to the PTAM-encoding sequences, or any partsthereof, are used to detect, decrease, or inhibit expression ofnaturally occurring PTAM. Although use of oligonucleotides comprisingfrom about 15 to 30 base pairs is described, essentially the sameprocedure is used with smaller or with larger sequence fragments.Appropriate oligonucleotides are designed using OLIGO 4.06 software(National Biosciences) and the coding sequence of PTAM. To inhibittranscription, a complementary oligonucleotide is designed from the mostunique 5′ sequence and used to prevent promoter binding to the codingsequence. To inhibit translation, a complementary oligonucleotide isdesigned to prevent ribosomal binding to the PTAM-encoding transcript.

Ix. Expression of PTAM

Expression and purification of PTAM is achieved using bacterial orvirus-based expression systems. For expression of PTAM in bacteria, cDNAis subcloned into an appropriate vector containing an antibioticresistance gene and an inducible promoter that directs high levels ofcDNA transcription. Examples of such promoters include, but are notlimited to, the trp-lac (tac) hybrid promoter and the T5 or T7bacteriophage promoter in conjunction with the lac operator regulatoryelement. Recombinant vectors are transformed into suitable bacterialhosts, e.g., BL21(DE3). Antibiotic resistant bacteria express PTAM uponinduction with isopropyl beta-D-thiogalactopyranoside (IPTG). Expressionof PTAM in eukaryotic cells is achieved by infecting insect or mammaliancell lines with recombinant Autographica californica nuclearpolyhedrosis virus (AcMNPV), commonly known as baculovirus. Thenonessential polyhedrin gene of baculovirus is replaced with cDNAencoding PTAM by either homologous recombination or bacterial-mediatedtransposition involving transfer plasmid intermediates. Viralinfectivity is maintained and the strong polyhedrin promoter drives highlevels of cDNA transcription. Recombinant baculovirus is used to infectSpodoptera frugiperda (Sf9) insect cells in most cases, or humanhepatocytes, in some cases. Infection of the latter requires additionalgenetic modifications to baculovirus. (See Engelhard, E. K. et al.(1994). Proc. Natl. Acad. Sci. USA 91:3224-3227; Sandig, V. et al.(1996) Hum. Gene Ther. 7:1937-1945.)

In most expression systems, PTAM is synthesized as a fusion proteinwith, e.g., glutathione S-transferase (GST) or a peptide epitope tag,such as FLAG or 6-His, permitting rapid, single-step, affinity-basedpurification of recombinant fusion protein from crude cell lysates. GST,a 26-kilodalton enzyme from Schistosoma japonicum, enables thepurification of fusion proteins on immobilized glutathione underconditions that maintain protein activity and antigenicity (AmershamPharmacia Biotech) Following purification, the GST moiety can beproteolytically cleaved from PTAM at specifically engineered sites.FLAG, an 8-amino acid peptide, enables immunoaffinity purification usingcommercially available monoclonal and polyclonal anti-FLAG antibodies(Eastman Kodak). 6-His, a stretch of six consecutive histidine residues,enables purification on metal-chelate resins (QIAGEN). Methods forprotein expression and purification are discussed in Ausubel (1995,supra, ch 10 and 16.) Purified PTAM obtained by these methods can beused directly in the following activity assay.

X. Functional Assays

PTAM function is assessed by expressing the sequences encoding PTAM atphysiologically elevated levels in mammalian cell culture systems. cDNAis subcloned into a mammalian expression vector containing a strongpromoter that drives high levels of cDNA expression. Vectors of choiceinclude pCMV SPORT (Life Technologies) and pCR3.1 (Invitrogen, CarlsbadCalif.), both of which contain the cytomegalovirus promoter. 5-10 μg ofrecombinant vector are transiently transfected into a human cell line,preferably of endothelial or hematopoietic origin, using either liposomeformulations or electroporation. 1-2 μg of an additional plasmidcontaining sequences encoding a marker protein are co-transfected.Expression of a marker protein provides a means to distinguishtransfected cells from nontransfected cells and is a reliable predictorof cDNA expression from the recombinant vector. Marker proteins ofchoice include, e.g., Green Fluorescent Protein (GFP; Clontech), CD64,or a CD64-GFP fusion protein. Flow cytometry (FCM), an automated, laseroptics-based technique, is used to identify transfected cells expressingGFP or CD64-GFP, and to evaluate properties, for example; theirapoptotic state. FCM detects and quantifies the uptake of fluorescentmolecules that diagnose events preceding or coincident with cell death.These events include changes in nuclear DNA content as measured bystaining of DNA with propidium iodide; changes in cell size andgranularity as measured by forward light scatter and 90 degree sidelight scatter; down-regulation of DNA synthesis as measured by decreasein bromodeoxyuridine uptake; alterations in expression of cell surfaceand intracellular proteins as measured by reactivity with specificantibodies; and alterations in plasma membrane composition as measuredby the binding of fluorescein-conjugated Annexin V protein to the cellsurface. Methods in flow cytometry are discussed in Ormerod, M. G.(1994) Flow Cytometry, Oxford, New York N.Y.

The influence of PTAM on gene expression can be assessed using highlypurified populations of cells transfected with sequences encoding PTAMand either CD64 or CD64-GFP. CD64 and CD64-GFP are expressed on thesurface of transfected cells and bind to conserved regions of humanimmunoglobulin G (IgG). Transfected cells are efficiently separated fromnontransfected cells using magnetic beads coated with either human IgGor antibody against CD64 (DYNAL, Lake Success N.Y.). mRNA can bepurified from the cells using methods well known by those of skill inthe art. Expression of mRNA encoding PTAM and other genes of interestcan be analyzed by northern analysis or microarray techniques.

XI. Production of PTAM Specific Antibodies

PTAM substantially purified using polyacrylamide gel electrophoresis(PAGE; see, e.g., Harrington, M. G. (1990) Methods Enzymol.182:488-495), or other purification techniques, is used to immunizerabbits and to produce antibodies using standard protocols.

Alternatively, the PTAM amino acid sequence is analyzed using LASERGENEsoftware (DNASTAR) to determine regions of high immunogenicity, and acorresponding oligopeptide is synthesized and used to raise antibodiesby means known to those of skill in the art. Methods for selection ofappropriate epitopes, such as those near the C-terminus or inhydrophilic regions are well described in the art. (See, e.g., Ausubel,1995, supra, ch. 11.)

Typically, oligopeptides 15 residues in length are synthesized using anABI 431 A Peptide Synthesizer (Perkin-Elmer) using fmoc-chemistry andcoupled to KLH (Sigma-Aldrich, St. Louis Mo.) by reaction withN-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS) to increaseimmunogenicity. (See, e.g., Ausubel, 1995, supra.) Rabbits are immunizedwith the oligopeptide-KLH complex in complete Freund's adjuvant.Resulting antisera are tested for antipeptide activity by, for example,binding the peptide to plastic, blocking with 1% BSA, reacting withrabbit antisera, washing, and reacting with radio-iodinated goatanti-rabbit IgG.

XII. Purification of Naturally Occurring PTAM Using Specific Antibodies

Naturally occurring or recombinant PTAM is substantially purified byimmunoaffinity chromatography using antibodies specific for PTAM. Animmunoaffinity column is constructed by covalently coupling anti-PTAMantibody to an activated chromatographic resin, such as CNBr-activatedSEPHAROSE (Amersham Pharmacia Biotech). After the coupling, the resin isblocked and washed according to the manufacturer's instructions.

Media containing PTAM are passed over the immunoaffinity column, and thecolumn is washed under conditions that allow the preferential absorbanceof PTAM (e.g., high ionic strength buffers in the presence ofdetergent). The column is eluted under conditions that disruptantibody/PTAM binding (e.g., a buffer of pH 2 to pH 3, or a highconcentration of a chaotrope, such as urea or thiocyanate ion), and PTAMis collected.

XIII. Identification of Molecules Which Interact with PTAM

PTAM, or biologically active fragments thereof, are labeled with 125IBolton-Hunter reagent. (See, e.g., Bolton et al. (1973) Biochem. J.133:529.) Candidate molecules previously arrayed in the wells of amulti-well plate are incubated with the labeled PTAM, washed, and anywells with labeled PTAM complex are assayed. Data obtained usingdifferent concentrations of PTAM are used to calculate values for thenumber, affinity, and association of PTAM with the candidate molecules.

Various modifications and variations of the described methods andsystems of the invention will be apparent to those skilled in the artwithout departing from the scope and spirit of the invention. Althoughthe invention has been described in connection with specific preferredembodiments, it should be understood that the invention as claimedshould not be unduly limited to such specific embodiments. Indeed,various modifications of the described modes for carrying out theinvention which are obvious to those skilled in molecular biology orrelated fields are intended to be within the scope of the followingclaims.

TABLE 1 Protein SEQ ID Nucleotide NO: SEQ ID NO: Clone ID LibraryFragments 1 9 012033 THP1PLB01 012033H1 (THP1PLB01), 37144OH1(LUNGNOT02), 1835003T6 (BRAINON01), 2184660T6 (SININOT01), 2355213F6 and2355213T6 (LUNGNOT20), 3564476H1 (SKINNOT05) 2 10 1209687 BRSTNOT021209687H1 (BRSTNOT02), 1212604T6 (BRSTTUT01), 2702873H1 (OVARTUT10) 3 111717058 UCMCNOT02 015033F1 and 015033R1 (HUVELPB01), 04185IR1(TBLYNOT01), 625952H1 (PGANNOT01), 1580781H1 (DUODNOT01), 1717058F6 and1717058H1 (UCMCNOT02) 4 12 1749964 STOMTUT02 455769F1 and 455769R1(KERANOT01), 734407R1 (TONSNOT01), 1688918F6 (PROSTUT10), 1749964H1(STOMTUT02), 1867108F6 (SKINBIT01), 1917583H1 (PROSNOT06), 1920136R6(BRSTTUT01), 2683294F6 (SINIUCT01) 5 13 1856357 PROSNOT18 1610265F6(COLNTUT06), 618761H1 (PGANNOT01), 732969R1 (LUNGNOT03), 874322H1(LUNGAST01), 968936H1 (BRSTNOT05), 1394835F6 (THYRNOT03), 1856357F6 and1856357H1 (PROSNOT18), 2788175H1 (BRSTNOT16), 2870537H1 (THYRNOT10),3359258H1 (PROSTUT16), 3931139H1 (PROSTUT09) 6 14 1871275 SKINBIT01081150F1 (SYNORAB01), 1509160F1 (LUNGNOT14), 1553311F1 (BLADTUT04),1871275H1 (SKINBIT01), SBAA02579F1 7 15 2645806 OVARTUT04 2239005F6(PANCTUT02), 3598925H1 (DRGTNOT01), 2645806F6 and 2645806H1 (OVARTUT04)8 16 3437773 PENCNOT05 148721F1 (FIBRNGT01), 1291051F6 (BRAINOT11),1979290R6 (LUNGTUT03), 2203762F6 (SPLNFET02), 3437773H1 (PENCNOT05)

TABLE 2 Protein Potential Seq ID Amino Acid Potential GlycosylationSignature Analytical NO: Residues Phosphorylation Sites Sites SequenceIdentification Methods 1 480 S56 T62 S70 T76 S84 N39 N82 N96 N152 M1-P19human TGN38 BLAST T90 S98 S112 T118 S126 N180 N208 N222 F385-A402homolog SPScan T132 S140 T146 S154 N373 N377 hTGN51 HMM T160 S168 T174S182 T188 S196 T202 S210 T216 S224 S238 T244 S258 S298 T331 T358 T363S365 S25 S47 S53 S95 T104 T109 T123 T137 S193 S221 T422 2 140 T8 T26 S53S57 S73 S98 nuclear BLAST transport factor NTF2 3 519 S185 T16 S33 S40S127 N300 K181-Y198 sorting nexin 2 PRINTS S147 S174 S227 T165 BLASTS179 T246 T296 T470 4 613 S233 S37 S39 S73 T84 novel VHS domain BLASTS183 T286 T287 S327 containing S115 T124 S225 S229 protein S435 S480S541 S551 5 719 S27 S78 T137 S243 S257 hook2 protein BLAST S413 T432T443 S654 S174 T234 S304 S316 S357 T575 S630 S700 T716 Y397 Y600 6 175S72 S101 T145 T171 S89 G2 TCR delta MOTIFS S139 T162 BLAST 7 142 T3 T9S54 T99 N123 nuclear BLAST transport factor NTF2 8 248 T126 T167 T54 T91S228 N73 G50-S57 Ras family MOTIFS K45-C248 member PFAM Rab4b BLASTPRINTS

TABLE 3 Polynucleotide Tissue Expression Disease Class Seq ID NO:(Fraction of Total) (Fraction of Total) Vector 9 Hematopoietic/Immune(0.314) Proliferative (0.571) PBLUESCRIPT Reproductive (0.171)Inflammation (0.485) Gastrointestinal (0.143) 10 Reproductive (0.500)Proliferative (0.643) PSPORT1 Cardiovascular (0.143) Inflammation(0.429) Hematopoietic/Immune (0.143) 11 Reproductive (0.256)Proliferative (0.651) pINCY Hematopoietic/Immune (0.174) Inflammation(0.279) Nervous (0.163) 12 Reproductive (0.245) Proliferative (0.687)pINCY Hematopoietic/Immune (0.147) Inflammation (0.284) Nervous (0.127)13 Reproductive (0.435) Proliferative (0.826) pINCY Gastrointestinal(0.130) Inflammation (0.217) Nervous (0.101) 14 Cardiovascular (0.233)Inflammation (0.535) pINCY Musculoskeletal (0.233) Cancer (0.395)Gastrointestinal (0.140) 15 Cardiovascular (0.308) Proliferative (0.846)pINCY Reproductive (0.231) Inflammation (0.308) Nervous (0.154)Gastrointestinal (0.154) 16 Nervous (0.245) Cancer (0.449) pINCYHematopoietic/Immune (0.184) Inflammation (0.367) Cardiovascular (0.163)

TABLE 4 Polynucleotide SEQ ID NO: Clone ID Library Library Description 9012033 THP1PLB01 Library was constructed using RNA isolated from THP-1cells cultured for 48 hours with 100 ng/ml phorbol ester (PMA), followedby a 4-hour culture in media containing 1 ug/ml LPS. THP-1 (ATCC TIB202) is a human promonocyte line derived from the peripheral blood of a1-year-old male with acute monocytic leukemia (ref: Int. J. Cancer(1980) 26:171). 10 1209687 BRSTNOT02 Library was constructed using RNAisolated from diseased breast tissue removed from a 55-year-oldCaucasian female during a unilateral extended simple mastectomy.Pathology indicated proliferative fibrocysytic changes characterized byapocrine metaplasia, sclerosing adenosis, cyst formation, and ductalhyperplasia without atypia. Pathology for the associated tumor tissueindicated an invasive grade 4 mammary adenocarcinoma. Patient historyincluded atrial tachycardia and a benign neoplasm. Family historyincluded cardiovascular and cerebrovascular disease. 11 1717058UCMCNOT02 Library was constructed using RNA isolated from mononuclearcells obtained from the umbilical cord blood of nine individuals. 121749964 STOMTUT02 Library was constructed using RNA isolated fromstomach tumor tissue obtained from a 68-year-old Caucasian female duringa partial gastrectomy. Pathology indicated a malignant lymphoma ofdiffuse large-cell type. Previous surgeries included cholecystectomy.Patient history included thalassemia. Family history included acuteleukemia, atherosclerotic coronary artery disease, and malignantneoplasm of the esophagus and stomach. 13 1856357 PROSNOT18 Library wasconstructed using RNA isolated from diseased prostate tissue removedfrom a 58-year-old Caucasian male during a radical cystectomy, radicalprostatectomy, and gastrostomy. Pathology indicated adenofibromatoushyperplasia; this tissue was associated with a grade 3 transitional cellcarcinoma. Patient history included angina and emphysema. Family historyincluded acute myocardial infarction, atherosclerotic coronary arterydisease, and type II diabetes. 14 1871275 SKINBIT01 Library wasconstructed using RNA isolated from diseased skin tissue of the leftlower leg. Patient history included erythema nodosum of the left lowerleg. 15 2645806 OVARTUT04 Library was constructed using RNA isolatedfrom ovarian tumor tissue removed from a 53-year-old Caucasian femaleduring a total abdominal hysterectomy, removal of the fallopian tubesand ovaries, regional lymph node excision, and peritoneal tissuedestruction. Pathology indicated grade 1 transitional cell carcinoma ofthe right ovary. The left ovary had a hemorrhagic corpus luteum. Theuterus had multiple leiomyomas (1 submucosal, 11 intramural), and theendometrium was inactive. The cul-de-sac contained abundant histiocytesand rare clusters of mesothelial cells. Patient history included breastfibrosclerosis and chronic stomach ulcer. Family history included acutestomach ulcer with perforation, breast cancer, bladder cancer,rectal/anal cancer, benign hypertension, coronary angioplasty, andhyperlipidemia. 16 3437773 PENCNOT05 Library was constructed using RNAisolated from penis left corpus cavernosum tissue removed from a male.

TABLE 5 Program Description Reference Parameter Threshold ABI A programthat removes vector sequences and Perkin-Elmer Applied Biosystems,FACTURA masks ambiguous bases in nucleic acid Foster City, CA.sequences. ABI/ A Fast Data Finder useful in comparing and Perkin-ElmerApplied Biosystems, Mismatch <50% PARACEL annotating amino acid ornucleic acid Foster City, CA; Paracel Inc., Pasadena, CA. FDF sequences.ABI A program that assembles nucleic acid Perkin-Elmer AppliedBiosystems, AutoAssembler sequences. Foster City, CA. BLAST A BasicLocal Alignment Search Tool useful in Altschul, S. F. et al. (1990) J.Mol. Biol. ESTs: Probability value = 1.0E-8 sequence similarity searchfor amino acid and 215:403-410; Altschul, S. F. et al. (1997) or lessnucleic acid sequences. BLAST includes five Nucleic Acids Res.25:3389-3402. Full Length sequences: Probability functions: blastp,blastn, blastx, tblastn, and value = 1.0E-10 or less tblastx. FASTA APearson and Lipman algorithm that searches Pearson, W. R. and D. J.Lipman (1988) Proc. ESTs: fasta E value = 1.06E-6 for similarity betweena query sequence and a Natl. Acad Sci. 85:2444-2448; Pearson, W. R.Assembled ESTs: fasta Identity = group of sequences of the same type.FASTA (1990) Methods Enzymol. 183:63-98; and 95% or greater and Matchcomprises as least five functions: fasta, tfasta, Smith, T. F. and M. S.Waterman (1981) Adv. length = 200 bases or greater; fastx fastx, tfastx,and ssearch. Appl. Math. 2:482-489. E value = 1.0E-8 or less Full Lengthsequences: fastx score = 100 or greater BLIMPS A BLocks IMProvedSearcher that matches a Henikoff, S. and J. G. Henikoff, Nucl. AcidRes., Score = 1000 or greater; Ratio of sequence against those in BLOCKSand 19:6565-72, 1991. J. G. Henikoff and S. Score/Strength = 0.75 orlarger; PRINTS databases to search for gene families, Henikoff (1996)Methods Enzymol. 266:88-105; and Probability value = 1.0E-3 or sequencehomology, and structural fingerprint and Attwood, T. K. et al. (1997) J.Chem. Inf. less regions. Comput. Sci. 37:417-424. PFAM A Hidden MarkovModels-based application Krogh, A. et al. (1994) J. Mol. Biol.,235:1501- Score = 10-50 bits, depending on useful for protein familysearch. 1531; Sonnhammer, E. L. L. et al. (1988) individual proteinfamilies Nucleic Acids Res. 26:320-322. ProfileScan An algorithm thatsearches for structural and Gribskov, M. et al. (1988) CABIOS 4:61-66;Score = 4.0 or greater sequence motifs in protein sequences thatGribskov, et al. (1989) Methods Enzymol. match sequence patterns definedin Prosite. 183:146-159; Bairoch, A. et al. (1997) Nucleic Acids Res.25:217-221. Phred A base-calling algorithm that examines Ewing, B. etal. (1998) Genome automated sequencer traces with high Res. 8:175-185;Ewing, B. and P. sensitivity and probability. Green (1998) Genome Res.8:186-194. Phrap A Phils Revised Assembly Program including Smith, T. F.and M. S. Waterman (1981) Adv. Score = 120 or greater; Match SWAT andCrossMatch, programs based on Appl. Math. 2:482-489; Smith, T. F. and M.S. length = 56 or greater efficient implementation of the Smith-Waterman (1981) J. Mol. Biol. 147:195-197; Waterman algorithm, useful insearching and Green, P., University of Washington, sequence homology andassembling DNA Seattle, WA. sequences. Consed A graphical tool forviewing and editing Phrap Gordon, D. et al. (1998) Genome assembliesRes. 8:195-202. SPScan A weight matrix analysis program that scansNielson, H. et al. (1997) Protein Engineering Score = 5 or greaterprotein sequences for the presence of secretory 10:1-6; Claverie, J. M.and S. Audie (1997) signal peptides. CABIOS 12:431-439. Motifs A programthat searches amino acid sequences Bairoch et al. supra; Wisconsin forpatterns that matched those defined in Package Program Manual, versionProsite. 9, page M51-59, Genetics Computer Group, Madison, WI.

1. An isolated polynucleotide encoding a polypeptide selected from thegroup consisting of: a) a polypeptide comprising an amino acid sequenceof SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7 or SEQ ID NO:8, and b) a polypeptide comprising an amino acid sequence at least 90%identical to an amino acid sequence of SEQ ID NO: 2, SEQ ID NO: 7 or SEQID NO:
 8. 2. A recombinant polynucleotide comprising a promoter sequenceoperably linked to the polynucleotide of claim
 1. 3. A cell transformedwith the recombinant polynucleotide of claim
 2. 4. A method of producinga polypeptide selected from the group consisting of: a) a polypeptidecomprising an amino acid sequence of SEQ ID NO: 2, SEQ ID NO: 3, SEQ IDNO: 5, SEQ ID NO: 7 or SEQ ID NO: 8, and b) a polypeptide comprising anamino acid sequence at least 90% identical to an amino acid sequence ofSEQ ID NO: 2, SEQ ID NO: 7 or SEQ ID NO: 8, the method comprising: i)culturing a cell under conditions suitable for expression of thepolypeptide, wherein said cell is transformed with the polynucleotide ofclaim 1 operably linked to a promoter sequence, and ii) recovering thepolypeptide so expressed.
 5. An isolated polynucleotide selected fromthe group consisting of: a) a polynucleotide comprising a polynucleotidesequence of SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13,SEQ ID NO: 15 or SEQ ID NO: 16, b) a polynucleotide comprising apolynucleotide sequence at least 90% identical to a polynucleotidesequence of SEQ ID NO: 10, SEQ ID NO: 15 or SEQ ID NO: 16, c) apolynucleotide complementary to a polynucleotide of a), d) apolynucleotide complementary to a polynucleotide of b) and e) an RNAequivalent of a)-d).
 6. A method of detecting a target polynucleotide ina sample, said target polynucleotide having a sequence of apolynucleotide of claim 5, the method comprising: a) hybridizing thesample with a probe comprising at least 20 contiguous nucleotidescomprising a sequence complementary to said target polynucleotide in thesample, and which probe specifically hybridizes to said targetpolynucleotide, under conditions whereby a hybridization complex isformed between said probe and said target polynucleotide, and b)detecting the presence or absence of said hybridization complex, and,optionally, if present, the amount thereof.
 7. A method of claim 6,wherein the probe comprises at least 60 contiguous nucleotides.
 8. Amethod of detecting a target polynucleotide in a sample, said targetpolynucleotide having a sequence of a polynucleotide of claim 5, themethod comprising: a) amplifying said target polynucleotide usingpolymerase chain reaction amplification, and b) detecting the presenceor absence of said amplified target polynucleotide and optionally, ifpresent, the amount thereof.
 9. An isolated polynucleotide encoding apolypeptide comprising an amino acid sequence selected from the groupconsisting of SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7 andSEQ ID NO:
 8. 10. An isolated polynucleotide of claim 9 comprising apolynucleotide sequence selected from the group consisting of SEQ ID NO:10, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15 and SEQ ID NO:
 16. 11. Amethod of screening a compound for effectiveness in altering expressionof a target polynucleotide, wherein said target polynucleotide comprisesa polynucleotide sequence of claim 5, the method comprising: a)contacting a sample comprising the target polynucleotide with, underconditions suitable for the expression of the target polynucleotide, b)detecting altered expression of the target polynucleotide, and c)comparing the expression of the target polynucleotide in the presence ofvarying amounts of the compound and in the absence of the compound.